Fowl production by administration of a synthetic bioensemble of microbes or purified strains thereof

ABSTRACT

The disclosure relates to isolated microorganisms-including novel strains of the microorganisms-microbial ensembles, and compositions comprising the same. Furthermore, the disclosure teaches methods of utilizing the described microorganisms, microbial ensembles, and compositions comprising the same, in methods for modulating the production of poultry, disease resistance, and egg yield. In particular aspects, the disclosure provides methods of increasing feed efficiency, and methods of preventing colonization of pathogenic microbes.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a U.S. National Stage Application under 35 U.S.C. § 371 of International PCT Application No. PCT/US2018/056563, filed on Oct. 18, 2018, which claims priority to and benefit of U.S. Provisional Application No. 62/574,031, filed on Oct. 18, 2017; each of which are incorporated herein by reference in their entirety.

FIELD

The present disclosure relates to isolated and biologically pure microorganisms that have applications, inter alia, in the farming of fowl or poultry. The disclosed microorganisms can be utilized in their isolated and biologically pure states, as well as being formulated into compositions. Furthermore, the disclosure provides bioensembles, containing at least two members of the disclosed microorganisms, as well as methods of utilizing said bioensembles. Furthermore, the disclosure provides for methods of modulating the fowl or poultry microbiome to modulate the immune system.

STATEMENT REGARDING SEQUENCE LISTING

The sequence listing associated with this application is provided in text format in lieu of a paper copy, and is hereby incorporated by reference into the specification. The name of the text file containing the sequence listing is ASBI_012_01US_ST25.txt. The text file is 165 kb, was created on Apr. 17, 2020, and is being submitted electronically via EFS-Web.

BACKGROUND

The global population is predicted to increase to over 9 billion people by the year 2050 with a concurrent reduction in the quantity of land, water, and other natural resources available per capita. Projections indicate that the average domestic income will also increase, with the projected rise in the GDP of China and India. The desire for a diet richer in animal-source proteins rises in tandem with increasing income, thus the global livestock sector will be charged with the challenge of producing more animal products using fewer resources. The Food and Agriculture Organization of the United Nations predict that 70% more food will have to be produced, yet the area of arable land available will decrease. It is clear that the food output per unit of resource input will have to increase considerably in order to support the rise in population.

Over recent decades the farm industry has seen fast growth in the meat sector, which has been underpinned by rising demand for poultry meat, which has consistently increased at about three times the rate of population growth over each of the past five decades.

Poultry meat, eggs, and components thereof are predominantly utilized in the preparation of foodstuffs in many different forms. There have been many strategies to improve poultry and egg production through nutritional modulations, hormone treatments, changes in animal management, and selective breeding; however, the need for more efficient production of edible poultry foodstuffs per animal is required.

Identifying compositions and methods for sustainably increasing poultry and egg production while balancing animal health and wellbeing have become imperative to satisfy the needs of everyday humans in an expanding population. Increasing the worldwide production of poultry by scaling up the total number of poultry on farms would not only be economically infeasible for many parts of the world, but would further result in negative environmental consequences as the poultry sector's growth and trends towards intensification and concentration have already given rise to a number of environmental concerns, led predominantly by the production of far more waste than can be managed by land disposal.

Population densities of poultry in large farms are often accompanied by an increased incidence of microbial pathogens that place the poultry yield at risk, and further place the ultimate consumer of the poultry at risk in instances of zoonotic pathogens such as those of Clostridium and Salmonella. Considering the widespread occurrence of many zoonotic pathogens, it is unlikely that poultry can be completely protected from exposure. Research has focused on investigative means of increasing resistance to colonization in poultry exposed to these pathogens. Furthermore, large farm poultry operations turn out large flocks that exhibit a high degree of variability in size, health, meat content due at least in part to the great degree of variability exhibited in the diversity of the reproductive and gut microbiomes.

Thus, meeting global poultry yield expectations, by simply scaling up current high-input agricultural systems—utilized in most of the developed world—is simply not feasible.

There is therefore an urgent need in the art for improved methods of increasing poultry and egg production, while also mitigating the colonization and spread of microbial pathogens.

SUMMARY OF THE DISCLOSURE

In some embodiments, the disclosure is generally drawn to a method for improving one or more desirable traits in fowl, the method comprising: (a) administering to a fowl an effective amount of a microbial composition comprising: (i) a purified microbial population that comprises one or more bacteria with a 16S nucleic acid sequence that shares at least 97% sequence identity with a nucleic acid sequence selected from SEQ ID NOs: 1-50 and 59-387 and/or one or more fungi with an ITS nucleic acid sequence that shares at least 97% sequence identity with a nucleic acid sequence selected from SEQ ID NOs: 51-58, and (ii) a carrier suitable for fowl administration; wherein the purified microbial population is present in the microbial composition in an amount effective to improve the one or more desirable traits as compared to a fowl not having been administered the microbial composition; and wherein the improvement of the one or more desirable traits is an improvement in the innate immune response, an improvement in incidence of normal gastrointestinal morphology, an improvement in growth rate, an improvement in total body mass, an improvement in feed conversion ratio, an improvement in pathogen exclusion, an improvement in competitive exclusion against pathogens, a reduction in mortality, a reduction in flock variability, an improvement in antimicrobial production, an improvement in stimulating the production of B cells, an improvement in stimulating the production of lymphocytes, an improvement in length of villi, and an improvement in expression of inflammatory cytokines.

In some embodiments, the fowl is a broiler. In some embodiments, the one or more bacteria and/or the one or more fungi have a MIC score of at least about 0.1.

In some embodiments, the purified microbial population comprises a bacterium with a 16S nucleic acid sequence sharing at least 97% identity with SEQ ID NO:386. In some embodiments, the purified microbial population comprises a bacterium with a 16S nucleic acid sequence sharing at least 97% identity with SEQ ID NO:387. In some embodiments, the purified microbial population further comprises one or more bacteria with a 16S nucleic acid sequence sharing at least 97% sequence identity with nucleic acid sequences selected from the group consisting of SEQ ID NO:13, SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:31, SEQ ID NO:369, SEQ ID NO:374, and SEQ ID NO:348. In some aspects, the purified microbial population comprises one or more bacteria with a 16S nucleic acid sequence sharing at least 97% sequence identity with SEQ ID NO:386 and SEQ ID NO:387. In some aspects, the purified microbial population comprises one or more bacteria with a 16S nucleic acid sequence comprising SEQ ID NO:386 and SEQ ID NO:387. In some aspects, the purified microbial population comprises one or more bacteria with a 16S nucleic acid sequence selected from the group consisting of SEQ ID NO:13, SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:31, SEQ ID NO:369, SEQ ID NO:374, and SEQ ID NO:348. In some embodiments the purified microbial population further comprises one or more bacteria with a 16S nucleic acid sequence sharing at least 97% sequence identity with nucleic acid sequences selected from the group consisting of SEQ ID NO:1 and SEQ ID NO:3. In some embodiments, the purified microbial population comprises one or more bacteria with a 16S nucleic acid sequence sharing at least 97% sequence identity with SEQ ID NO:386 and SEQ ID NO:387. In some embodiments, the purified microbial population comprises one or more bacteria with a 16S nucleic acid sequence comprising SEQ ID NO:386 and SEQ ID NO:387. In some embodiments, the purified microbial population comprises one or more bacteria with a 16S nucleic acid sequence selected from the group consisting of SEQ ID NO:1 and SEQ ID NO:3.

In some embodiments, the microbial composition is formulated as an encapsulation, tablet, capsule, pill, feed additive, food ingredient, food preparation, food supplement, water additive, water-mixed additive, heat-stabilized additive, moisture-stabilized additive, pre-pelleted feed additive, pelleted feed additive, post-pelleting-applied feed additive, consumable solution, consumable spray additive, consumable solid, consumable gel, injection, suppository, drench, bolus, or combination thereof.

In some embodiments, the improvement of the one or more desirable traits is an improvement in antimicrobial production. In some embodiments, the improvement of antimicrobial production is an improvement of antimicrobial production in the gastrointestinal tract. In some embodiments, the administering of a purified microbial population comprises administering a first microbial composition and a second microbial compositions.

In some embodiments, the microbial composition elicits a decrease in the variability of the number of unique species in the gastrointestinal tract. In some embodiments, the decrease in the variability of the number of unique species is a reduction of the total number of unique species of microbes to between about 50 and 400 species.

In some embodiments, the disclosure is generally drawn to a microbial composition comprising (i) a purified microbial population that comprises one or more bacteria with a 16S nucleic acid sequence that shares at least 97% sequence identity with a nucleic acid sequence selected from SEQ ID NOs: 1-50 and 59-387 and/or one or more fungi with an ITS nucleic acid sequence that shares at least 97% sequence identity with a nucleic acid sequence selected from SEQ ID NOs: 51-58, and (ii) a carrier suitable for fowl administration; wherein the purified microbial population is present in the microbial composition in an amount effective to improve the one or more desirable traits as compared to a fowl not having been administered the microbial composition; and wherein the improvement of the one or more desirable traits is an improvement in the innate immune response, an improvement in incidence of normal gastrointestinal morphology, an improvement in growth rate, an improvement in total body mass, an improvement in feed conversion ratio, an improvement in pathogen exclusion, an improvement in competitive exclusion against pathogens, a reduction in mortality, a reduction in flock variability, an improvement in antimicrobial production, an improvement in stimulating the production of B cells, an improvement in stimulating the production of lymphocytes, an improvement in length of villi, and an improvement in expression of inflammatory cytokines; and wherein at least one of the one or more bacteria and/or at least one of the one or more fungi is desiccated.

In some aspects, the fowl is a broiler. In some aspects the one or more bacteria and/or the one or more fungi have a MIC score of at least about 0.1.

In some embodiments, the purified microbial population comprises a bacterium with a 16S nucleic acid sequence sharing at least 97% identity with SEQ ID NO:386. In some embodiments, the purified microbial population comprises a bacterium with a 16S nucleic acid sequence sharing at least 97% identity with SEQ ID NO:387. In some embodiments, the purified microbial population further comprises one or more bacteria with a 16S nucleic acid sequence sharing at least 97% sequence identity with nucleic acid sequences selected from the group consisting of SEQ ID NO:13, SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:31, SEQ ID NO:369, SEQ ID NO:374, and SEQ ID NO:348. In some aspects, the purified microbial population comprises one or more bacteria with a 16S nucleic acid sequence sharing at least 97% sequence identity with SEQ ID NO:386 and SEQ ID NO:387. In some aspects, the purified microbial population comprises one or more bacteria with a 16S nucleic acid sequence comprising SEQ ID NO:386 and SEQ ID NO:387. In some aspects, the purified microbial population comprises one or more bacteria with a 16S nucleic acid sequence selected from the group consisting of SEQ ID NO:13, SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:31, SEQ ID NO:369, SEQ ID NO:374, and SEQ ID NO:348. In some embodiments the purified microbial population further comprises one or more bacteria with a 16S nucleic acid sequence sharing at least 97% sequence identity with nucleic acid sequences selected from the group consisting of SEQ ID NO:1 and SEQ ID NO:3. In some embodiments, the purified microbial population comprises one or more bacteria with a 16S nucleic acid sequence sharing at least 97% sequence identity with SEQ ID NO:386 and SEQ ID NO:387. In some embodiments, the purified microbial population comprises one or more bacteria with a 16S nucleic acid sequence comprising SEQ ID NO:386 and SEQ ID NO:387. In some embodiments, the purified microbial population comprises one or more bacteria with a 16S nucleic acid sequence selected from the group consisting of SEQ ID NO:1 and SEQ ID NO:3.

In some embodiments, the microbial composition is formulated as an encapsulation, tablet, capsule, pill, feed additive, food ingredient, food preparation, food supplement, water additive, water-mixed additive, heat-stabilized additive, moisture-stabilized additive, pre-pelleted feed additive, pelleted feed additive, post-pelleting-applied feed additive, consumable solution, consumable spray additive, consumable solid, consumable gel, injection, suppository, drench, bolus, or combination thereof.

In some embodiments, the improvement of the one or more desirable traits is an improvement in antimicrobial production. In some embodiments, the improvement of antimicrobial production is an improvement of antimicrobial production in the gastrointestinal tract.

In some embodiments, the microbial composition elicits a decrease in the variability of the number of unique species in the gastrointestinal tract. In some embodiments, the decrease in the variability of the number of unique species is a reduction of the total number of unique species of microbes to between about 50 and 400 species.

Budapest Treaty on the International Recognition of the Deposit of Microorganisms for the Purpose of Patent Procedures

Some microorganisms described in this application were deposited with the United States Department of Agriculture (USDA) Agricultural Research Service (ARS) Culture Collection (NRRL®), located at 1815 N. University St., Peoria, Ill. 61604, USA. Some microorganisms described in this application were deposited with the Bigelow National Center for Marine Algae and Microbiota, located at 60 Bigelow Drive, East Boothbay, Me. 04544, USA. Some microorganisms described in this application were deposited with the American Type Culture Collection (ATCC), located at 10801 University Boulevard, Manassas, Va. 20108, USA.

The deposits were made under the terms of the Budapest Treaty on the International Recognition of the Deposit of Microorganisms for the Purposes of Patent Procedure. The NRRL®, ATCC, and Bigelow National Center for Marine Algae and Microbiota accession numbers for the aforementioned Budapest Treaty deposits are provided in Table 2. The accession numbers and corresponding dates of deposit for the microorganisms described in this application are separately provided in Table 15.

The strains designated in the below table have been deposited in the labs of Ascus Biosciences, Inc. since at least Mar. 1, 2016. Strains comprising SEQ ID NOs:386 and 387 were isolated prior to, and stored since October 2017.

In Table 1, the closest predicted hits for taxonomy of the microbes are listed in columns 2 and 5. Column 2 is the top taxonomic hit predicated by BLAST, and column 5 is the top taxonomic hit for genus+species predicted by BLAST. The strains designated in the below table have been deposited in the labs of Ascus Biosciences, Inc. since at least Mar. 1, 2016.

Table 1 lists strain designations of the bacteria and fungi of the present disclosure. If a letter in parentheses follows any of the strain designations, then that indicates that each of those strains have variants that share at least 97% sequence identity with the reference strain with the (A) parenthetical. Ascusbbr_5796(A) has two variants, Ascusbbr_5796(B) and Ascusbbr_5796(C) that share 97.8% and 98.2% sequence identity, respectively, with Ascusbbr_5796(A). Ascusbbr_14690(A) has two variants, Ascusbbr_14690(B) and Ascusbbr_14690(C) that share 97.8% and 98.2% sequence identity, respectively, with Ascusbbr_14690(A). Ascusbbr_38717(A) shares 98.6% sequence identity with Ascusbbr_38717(B). Ascusbbr_33(A) shares 98.2% sequence identity with Ascusbbr_33(B). Ascusbbr_409(B), Ascusbbr_409(C), Ascusbbr_409(D), share 98.2%, 97.3%, and 97.8% sequence identity, respectively, with Ascusbbr_409(B). Ascus_331885(B) and Ascus_331885(C) share 97.8% and 97.3% sequence identity, respectively, with Ascus_331885(A). Ascusbbr_247(A) shares 97.8% sequence identity with Ascusbbr_247(B). Ascusbbr_10593(A) shares 99.6% sequence identity with Ascusbbr_10593(B). Ascusbbr_32731(A) shares 97.3% sequence identity with Ascusbbr_32731(B). Ascusbbr_1436(A) shares 97.8% sequence identity with Ascusbbr_1436(B). Ascusbbr_265(A) shares 99.6% sequence identity with Ascusbbr_265(B).

TABLE 1 Microbes of the present disclosure, including bacteria (1-99) and fungi (100-107). Se- quence BLAST Identi- Taxonomic fier for Predicted Closest BLAST BLAST Top Hit BLAST Asso- Taxa of Isolated Taxonomic % Query w/Genus + % Query Strain ciated MIC Microbes Top Hit Ident. Cover Species Ident. Cover Designation Marker Score 1. Lactobacillus Lactobacillus 98% 100% Lactobacillus 98% 100% Ascusbbr_4729 SEQ ID 0.76676 (Genus) crispatus crispatus NO: 1 2. Lachnospiraceae Bacterium ic1296 98%  91% Ruminococcus 95%  98% Ascusbbr_339 SEQ ID 0.62924 Clostridium gnavus NO: 2 Cluster XIVa (Family + Cluster) 3. Lactobacillus Lactobacillus 100%  100% Lactobacillus 100%  100% Ascusbbr_5796(A) SEQ ID 0.61325 (Genus) crispatus crispatus NO: 3 4. Lactobacillus Lactobacillus 100%  100% Lactobacillus 100%  100% Ascusbbr_5796(B) SEQ ID 0.61325 (Genus) crispatus crispatus NO: 369 5. Lactobacillus Lactobacillus 100%  100% Lactobacillus 100%  100% Ascusbbr_5796(C) SEQ ID 0.61325 (Genus) crispatus crispatus NO: 370 6. Lactobacillus Lactobacillus 99% 100% Lactobacillus 99% 100% Ascusbbr_38717(A) SEQ ID 0.59229 (Genus) vaginalis vaginalis NO: 4 7. Lactobacillus Lactobacillus 99% 100% Lactobacillus 99% 100% Ascusbbr_38717(B) SEQ ID 0.59229 (Genus) vaginalis vaginalis NO: 373 8. Lactobacillus Lactobacillus 99%  98% Lactobacillus 99%  98% Ascusbbr_170211 SEQ ID 0.58403 (Genus) vaginalis vaginalis NO: 5 9. Lactobacillus Lactobacillus 99% 100% Lactobacillus 99% 100% Ascusbbr_1686 SEQ ID 0.57845 (Genus) johnsonii johnsonii NO: 6 10. Faecalibacterium Faecalibacterium 90%  98% Faecalibacterium 89%  97% Ascusbbr_1789 SEQ ID 0.56099 (Genus) sp. prausnitzii NO: 7 11. Lactobacillus Lactobacillus 99% 100% Lactobacillus 99% 100% Ascusbbr_3820 SEQ ID 0.55862 (Genus) johnsonii johnsonii NO: 8 12. Hydrogenoanaero Clostridium sp. 91%  98% Butyrivibrio 86%  82% Ascusbbr_173 SEQ ID 0.55675 bacterium hungatei NO: 9 (Genus) 13. Peptostrepto- Clostridium sp. 92% 100% [Eubacterium] 91%  98% Ascusbbr_3089 SEQ ID 0.55548 coccaceae tenue NO: 10 Clostridium Cluster XI (Family + Cluster) 14. Acrocarpospora Nonomuraea sp. 99%  88% Microbispora 95% 100% Ascusbbr_167 SEQ ID 0.5442 (Genus) rosea NO: 11 15. Lactobacillus Lactobacillus 99%  98% Lactobacillus 99%  98% Ascusbbr_301568 SEQ ID 0.53873 (Genus) helveticus helveticus NO: 12 16. Bacillus (Genus) Bacillus 99% 100% Bacillus 99% 100% Ascusbbr_33(A) SEQ ID 0.53686 subtilis subtilis NO: 13 17. Bacillus (Genus) Bacillus 99% 100% Bacillus 99% 100% Ascusbbr_33(B) SEQ ID 0.53686 subtilis subtilis NO: 374 18. Lactobacillus Lactobacillus 99%  95% Lactobacillus 99%  95% Ascusbbr_25200 SEQ ID 0.52435 (Genus) coleohominis coleohominis NO: 14 19. Subdoligranulum Bacterium ic1340 90%  98% Anaerofilum 88%  91% Ascusbbr_84 SEQ ID 0.52174 (Genus) pentosovorans NO: 15 20. Subdoligranulum Firmicutes 99% 100% Faecalibacterium 96% 100% Ascusbbr 136 SEQ ID 0.51373 (Genus) bacterium prausnitzii NO: 16 21. Lachnospiraceae Clostridium sp. 95% 100% Eubacterium 94%  98% Ascusbbr_128 SEQ ID 0.51348 Clostridium fissicatena NO: 17 Cluster XIVa (Family + Cluster) 22. Lactobacillus Lactobacillus 99%  95% Lactobacillus 99%  95% Ascusbbr_322104 SEQ ID 0.50724 (Genus) coleohominis coleohominis NO: 18 23. Lactobacillus Lactobacillus 100%  100% Lactobacillus 100%  100% Ascusbbr_409(A) SEQ ID 0.50572 (Genus) reuteri reuteri NO: 19 24. Lactobacillus Lactobacillus 100%  100% Lactobacillus 100%  100% Ascusbbr_409(B) SEQ ID 0.50572 (Genus) reuteri reuteri NO: 375 25. Lactobacillus Lactobacillus 100%  100% Lactobacillus 100%  100% Ascusbbr_409(C) SEQ ID 0.50572 (Genus) reuteri reuteri NO: 376 26. Lactobacillus Lactobacillus 100%  100% Lactobacillus 100%  100% Ascusbbr_409(D) SEQ ID 0.50572 (Genus) reuteri reuteri NO: 377 27. Leuconostoc Leuconostoc 99% 100% Leuconostoc 99% 100% Ascusbbr_127 SEQ ID 0.4955 (Genus) mesenteroides mesenteroides NO: 20 28. Lachnospiracea Lachnospiraceae 96% 100% Eubacterium 91% 100% Ascusbbr_14834 SEQ ID 0.49531 incertae sedis bacterium hallii NO: 21 (Genus) 29. Lactobacillus Lactobacillus 99% 100% Lactobacillus 99% 100% Ascusbbr_331885(A) SEQ ID 0.49378 (Genus) reuteri reuteri NO: 22 30. Lactobacillus Lactobacillus 99% 100% Lactobacillus 99% 100% Ascusbbr_331885(B) SEQ ID 0.49378 (Genus) reuteri reuteri NO: 378 31. Lactobacillus Lactobacillus 99% 100% Lactobacillus 99% 100% Ascusbbr_331885(C) SEQ ID 0.49378 (Genus) reuteri reuteri NO: 379 32. Anaerofilum Clostridiales 88%  97% Ruthenibacterium 88%  98% Ascusbbr_31 SEQ ID 0.48633 (Genus) bacterium lactatiformans NO: 23 33. Lachnospiracea Blautia 96% 100% Blautia 96% 100% Ascusbbr_2307 SEQ ID 0.48546 incertae sedis hydroge- hydroge- NO: 24 (Genus) notrophica notrophica 34. Lachnospiraceae Clostridium 98% 100% Clostridium 91% 100% Ascusbbr_247(A) SEQ ID 0.48546 Clostridium saccharolyticum- clostridioforme NO: 25 Cluster like K10 XIVa (Family + Cluster) 35. Lachnospiraceae Clostridium 98% 100% Clostridium 91% 100% Ascusbbr_247(B) SEQ ID 0.48546 Clostridium saccharolyticum- clostridioforme NO: 380 Cluster like K10 XIVa (Family + Cluster) 36. Microbacterium Pseudo- 95%  99% Pseudo- 99%  79% Ascusbbr_19 SEQ ID 0.47772 (Genus) clavibacter sp. clavibacter NO: 26 caeni 37. Verrucosispora Verrucosispora 99% 100% Verrucosispora 97%  98% Ascusbbr_69 SEQ ID 0.47757 (Genus) sp. wenchangensis NO: 27 38. Anaerofilum Faecalibacterium 93% 100% Faecalibacterium 93% 100% Ascusbbr_94 SEQ ID 0.46645 (Genus) prausnitzii prausnitzii NO: 28 39. Clostridium sensu Candidatus 90%  91% Peptoclostridium 89%  91% Ascusbbr_313454 SEQ ID 0.46594 stricto (Genus) Arthromitus sp difficile NO: 29 40. Lactobacillus Lactobacillus 96% 100% Lactobacillus 96% 100% Ascusbbr_351000 SEQ ID 0.46296 (Genus) helveticus helveticus NO: 30 41. Lactobacillus Lactobacillus 99% 100% Lactobacillus 99% 100% Ascusbbr_1436(A) SEQ ID 0.46076 (Genus) salivarius salivarius NO: 31 42. Lactobacillus Lactobacillus 99% 100% Lactobacillus 99% 100% Ascusbbr_1436(B) SEQ ID 0.46076 (Genus) salivarius salivarius NO: 383 43. Lachnospiraceae Roseburia 93% 100% Roseburia 93% 100% Ascusbbr_28 SEQ ID 0.46028 Clostridium inulinivorans inulinivorans NO: 32 Cluster XIVa (Family + Cluster) 44. Blautia Ruminococcus 94% 100% Ruminococcus 94% 100% Ascusbbr_144 SEQ ID 0.45742 (Genus) obeum obeum NO: 33 45. Lactobacillus Lactobacillus 99%  99% Lactobacillus 99%  99% Ascusbbr_42760(A) SEQ ID 0.43682 (Genus) oris oris NO: 34 46. Lactobacillus Lactobacillus 99%  99% Lactobacillus 99%  99% Ascusbbr_42760(B) SEQ ID 0.43682 (Genus) oris oris NO: 384 47. Lactobacillus Lactobacillus 99%  83% Lactobacillus 99%  83% Ascusbbr_134994 SEQ ID 0.434 (Genus) crispatus crispatus NO: 35 48. Lactobacillus Lactobacillus 94%  88% Lactobacillus 94%  88% Ascusbbr_358773 SEQ ID 0.43348 (Genus) reuteri reuteri NO: 36 49. Pseudomonas Pseudomonas 99% 100% Pseudomonas 99% 100% Ascusbbr_2503 SEQ ID 0.42622 (Genus) chengduensis chengduensis NO: 37 50. Sporobacter Syntropho- 86%  82% Clostridium 84%  82% Ascusbbr_312 SEQ ID 0.42622 (Genus) monadaceae sphenoides NO: 39 bacterium 51. Lactobacillus Lactobacillus 99%  83% Lactobacillus 99%  83% Ascusbbr_140914 SEQ ID 0.40935 (Genus) crispatus crispatus NO: 40 52. Lactobacillus Lactobacillus 98%  82% Lactobacillus 98%  82% Ascusbbr_257627 SEQ ID 0.40775 (Genus) salivarius salivarius NO: 41 53. Lactobacillus Lactobacillus 98%  82% Lactobacillus 98%  82% Ascusbbr_310088 SEQ ID 0.40576 (Genus) helveticus helveticus NO: 42 54. Lachnospiracea Blautia 96% 100% Blautia 96% 100% Ascusbbr_91 SEQ ID 0.40345 incertae sedis hydrogeno- hydrogeno- NO:43 (Genus) trophica trophica 55. Lactobacillus Lactobacillus 97%  83% Lactobacillus 97%  83% Ascusbbr_150100 SEQ ID 0.40128 (Genus) crispatus crispatus NO: 44 56. Lactobacillus Lactobacillus 97% 100% Lactobacillus 97% 100% Ascusbbr_252028 SEQ ID 0.3998 (Genus) vaginalis vaginalis NO: 45 57. Peptostrepto- Clostridium sp. 93% 100% Romboutsia 92% 100% Ascusbbr_2158 SEQ ID 0.39816 coccaceae lituseburensis NO: 46 Clostridium Cluster XI (Family + Cluster) 58. Lactobacillus Lactobacillus 96% 100% Lactobacillus 96% 100% Ascusbbr_373 SEQ ID 0.37614 (Genus) crispatus crispatus NO: 47 59. Lactobacillus Lactobacillus 98%  94% Lactobacillus 98%  94% Ascusbbr_1802 SEQ ID 0.37123 (Genus) johnsonii johnsonii NO: 48 60. Lactobacillus Lactobacillus 96% 100% Lactobacillus 96% 100% Ascusbbr_107 SEQ ID 0.37123 (Genus) reuteri reuteri NO: 49 61. Lactobacillus Lactobacillus 93%  83% Lactobacillus 93%  83% Ascusbbr_1727 SEQ ID 0.36309 (Genus) crispatus crispatus NO: 50 62. Corynebacterium Corynebacterium 100%  100% Corynebacterium 100%  100% Ascusbbr_226 SEQ ID 0.75897 (Genus) glutamicum glutamicum NO: 338 63. Streptococcus Streptococcus 97%  94% Streptococcus 97%  94% Ascusbbr_17 SEQ ID 0.62924 (Genus) hyovaginalis hyovaginalis NO: 339 64. Lactobacillus Lactobacillus 99% 100% Lactobacillus 99% 100% Ascusbbr_14690(A) SEQ ID 0.60061 (Genus) aviarius aviarius NO: 340 65. Lactobacillus Lactobacillus 99% 100% Lactobacillus 99% 100% Ascusbbr_14690(B) SEQ ID 0.60061 (Genus) aviarius aviarius NO: 371 66. Lactobacillus Lactobacillus 99% 100% Lactobacillus 99% 100% Ascusbbr_14690(C) SEQ ID 0.60061 (Genus) aviarius aviarius NO: 372 67. Corynebacterium Corynebacterium 100%  100% Corynebacterium 100%  100% Ascusbbr_18 SEQ ID 0.58366 (Genus) xerosis xerosis NO: 341 68. Peptostrepto- Romboutsia 98% 100% Romboutsia 98% 100% Ascusbbr_7363 SEQ ID 0.57242 coccaceae lituseburensis lituseburensis NO: 342 (Clostridium Cluster XI) (Family + Cluster) 69. Corynebacterium Corynebacterium 100%  100% Corynebacterium 100%  100% Ascusbbr_35 SEQ ID 0.49929 (Genus) falsenii falsenii NO: 343 70. Corynebacterium Corynebacterium 98%  97% Corynebacterium 98%  97% Ascusbbr_7779 SEQ ID 0.48127 (Genus) ammoniagenes ammoniagenes NO: 344 71. Lachnospiraceae Desulfoto- 96% 100% Clostridium 95% 100% Ascusbbr_10593(A) SEQ ID 0.47763 (Clostridium maculum sp. sphenoides NO: 345 Cluster XlVa) (Family + Cluster) 72. Lachnospiraceae Desulfoto- 96% 100% Clostridium 95% 100% Ascusbbr_10593(B) SEQ ID 0.47763 (Clostridium maculum sp. sphenoides NO: 381 Cluster XlVa) (Family + Cluster) 73. Lachnospiracea Eubacterium sp. 98% 100% Eubacterium 93%  98% Ascusbbr_32731(A) SEQ ID 0.47124 incertae sedis fissicatena NO: 346 (Genus) 74. Lachnospiracea Eubacterium sp. 98% 100% Eubacterium 93%  98% Ascusbbr_32731(B) SEQ ID 0.47124 incertae sedis fissicatena NO: 382 (Genus) 75. Ruminococcaceae Bacterium 89%  78% Rumini- 86%  79% Ascusbbr_359892 SEQ ID 0.39553 (Clostridium clostridium NO: 347 Cluster thermocellum III) (Family + Cluster) 76. Lactobacillus Lactobacillus 100%  100% Lactobacillus 100%  100% Ascusbbr_25721 SEQ ID 0.39537 (Genus) pentosus pentosus NO: 348 77. Streptococcus Swine fecal 100%  100% Streptococcus 99% 100% Ascusbbr_72076 SEQ ID 0.38425 (Genus) bacterium alactolyticus NO: 349 78. Lachnospiraceae Lachnospiraceae 91%  92% Blautia producta 89%  97% Ascusbbr_6097 SEQ ID 0.37484 (Clostridium bacterium NO: 350 Cluster XlVa) (Family + Cluster) 79. Lactobacillus Lactobacillus 100%  100% Lactobacillus 100%  100% Ascusbbr_265(A) SEQ ID 0.37167 (Genus) helveticus helveticus NO: 351 80. Lactobacillus Lactobacillus 100%  100% Lactobacillus 100%  100% Ascusbbr_265(B) SEQ ID 0.37167 (Genus) helveticus helveticus NO: 385 81. Paracoccus Paracoccus 99%  99% Paracoccus 99%  99% Ascusbbr_323376 SEQ ID 0.36852 (Genus) alcaliphilus alcaliphilus NO: 352 82. Cellulosilyticum Ruminococcus sp. 97% 100% Hydrogenoan 84%  98% Ascusbbr_36257 SEQ ID 0.36078 (Genus) aerobacterium NO: 353 saccharovorans 83. Blautia Blautia 89% 100% Blautia 89% 100% Ascusbbr_6957 SEQ ID 0.35528 (Genus) glucerasea glucerasea NO: 354 84. Corynebacterium Corynebacterium 99% 100% Corynebacterium 99% 100% Ascusbbr_38 SEQ ID 0.35488 (Genus) flavescens flavescens NO: 355 85. Lachnospiracea Eubacteriaceae 98%  92% Coprococcus 87%  99% Ascusbbr_13398 SEQ ID 0.34774 incertae sedis bacterium catus NO: 356 (Genus) 86. Corynebacterium Corynebacterium 100%  100% Corynebacterium 100%  100% Ascusbbr_57 SEQ ID 0.34405 (Genus) callunae callunae NO: 357 87. Corynebacterium Corynebacterium 99% 100% Corynebacterium 99% 100% Ascusbbr_285160 SEQ ID 0.32892 (Genus) stationis stationis NO: 358 88. Ruminococcus Clostridium sp. 92%  96% Blautia producta 91%  96% Ascusbbr_37385 SEQ ID 0.3236 (Genus) NO: 359 89. Lactobacillus Lactobacillus 92% 100% Lactobacillus 92% 100% Ascusbbr_118124 SEQ ID 0.31115 (Genus) intestinalis intestinalis NO: 360 90. Roseburia Bacterium 92%  99% Frisingicoccus 91% 100% Ascusbbr_32592 SEQ ID 0.29912 (Genus) AC2012 caecimuris NO: 361 91. Lachnospiraceae Clostridium sp. 90%  99% Eubacterium 92%  91% Ascusbbr_110856 SEQ ID 0.29418 (Clostridium ventriosum NO: 362 Cluster XlVa) (Family + Cluster) 92. Lachnospiraceae Clostridiales 99%  99% Clostridium 97%  99% Ascusbbr_185064 SEQ ID 0.21604 (Clostridium bacterium lactatifermentans NO: 363 Cluster XlVb) (Family + Cluster) 93. Clostridium sensu Clostridium sp. 99% 100% Clostridium 99%  99% Ascusbbr _3315 SEQ ID 0.20534 stricto (Genus) thermobutyricum NO: 364 94. Bacteroides dorei Bacteroides dorei 100%  100% Bacteroides dorei 100%  100% Ascusbbr_578 SEQ ID 0.74887 NO: 365 95. Lactobacillus Lactobacillus 95% 100% Lactobacillus 95% 100% Ascusbbr_21169 SEQ ID 0.47787 (Genus) reuteri reuteri NO: 366 96. Lactobacillus Lactobacillus 96%  98% Lactobacillus 96%  98% Ascusbbr_110856 SEQ ID 0.39178 (Genus) reuteri reuteri NO: 367 97. Lactobacillus Lactobacillus 100%  100% Lactobacillus 100%  100% Ascusbbr_830 SEQ ID 0.33782 (Genus) saerimneri saerimneri NO: 368 98. Clostridium Clostridium 99% 100% Clostridium 99% 100% Ascusbbr_2676 SEQ ID 0.40777 (Genus) beijerinckii beijerinckii NO: 386 99. Clostridium Clostridium 100%   99% Clostridium 100%   99% Ascusbbr_105932 SEQ ID 0.47763 (Genus) saccharolyticum saccharolyticum NO: 387 100. Nectriaceae Fusarium 100%  100% Fusarium 100%  100% Ascusfbr_15 SEQ ID 0.42622 (Family) annulatum annulatum NO: 51 101. Filobasidium Uncultured 100%  100% Cryptococcus 100%  100% Ascusfbr _131 SEQ ID 0.42622 floriforme fungus magnus NO: 52 (Genus + species) 102. Gibberella zeae Fusarium 100%  100% Fusarium 100%  100% Ascusfbr _26 SEQ ID 0.36913 (Genus + species) asiaticum asiaticum NO: 53 103. Alatospora Uncultured 83%  81% Gymnoascus 83%  81% Ascusfbr _2616 SEQ ID 0.33927 (Genus) Gymnoascus reesii NO: 54 104. Hypocreaceae Geotrichum sp. 100%  100% Geotrichum 100%  100% Ascusfbr _12 SEQ ID 0.32217 (Family) candidum NO: 55 105. Pichia Pichia 100%  100% Pichia 100%  100% Ascusfbr _53 SEQ ID 0.30645 fermentans fermentans fermentans NO: 56 (Genus + species) 106. Candida Candida 99% 100% Candida 99% 100% Ascusfbr _1379 SEQ ID 0.28513 railenensis railenensis railenensis NO: 57 (Genus + species) 107. Hypocreaceae Uncultured 100%  100% Geotrichum 100%  100% Ascusfbr _122 SEQ ID 0.25801 (Family) fungus candidum NO: 58

In some embodiments, the isolated microbial strains of the present disclosure further encompass mutants thereof. In some embodiments, the present disclosure further contemplates microbial strains having all of the identifying characteristics of the presently disclosed microbial strains.

TABLE 2 Microbial Deposits Corresponding to the Microbes of Table 1 Se- Se- quence quence Identi- Identi- fier for fier for Predicted Taxa Asso- Predicted Taxa Asso- of Isolated Strain ciated of Isolated Strain ciated Microbes Designation Marker Deposit # Microbes Designation Marker Deposit # Lactobacillus Ascusbbr_4729 SEQ ID PATENT201703004 Peptostrepto- Ascusbbr_2158 SEQ ID PTA-124039 (Genus) NO: 1 coccaceae NO: 46 Clostridium Cluster XI (Family + Cluster) Lachno- Ascusbbr_339 SEQ ID PTA-124016, Lactobacillus Ascusbbr_373 SEQ ID spiraceae NO: 2 PTA-124039 (Genus) NO: 47 Clostridium Cluster XIVa (Family + Cluster) Lactobacillus Ascusbbr_5796(A) SEQ ID PATENT201703001, Lactobacillus Ascusbbr_1802 SEQ ID (Genus) NO: 3 PATENT201703003, (Genus) NO: 48 PATENT201703004, B-67267 Lactobacillus Ascusbbr_5796(B) SEQ ID PTA-124039 (Genus) NO: 369 Lactobacillus Ascusbbr_5796(C) SEQ ID PATENT201703002 (Genus) NO: 370 Lactobacillus Ascusbbr_38717(A) SEQ ID PATENT201703002, Lactobacillus Ascusbbr_107 SEQ ID PATENT201703002 (Genus) NO: 4 PATENT201703003, (Genus) NO: 49 PATENT201703004, B-67268 Lactobacillus Ascusbbr_38717(B) SEQ ID PATENT201703001 (Genus) NO: 373 Lactobacillus Ascusbbr_170211 SEQ ID PATENT201703002 Lactobacillus Ascusbbr_1727 SEQ ID (Genus) NO: 5 (Genus) NO: 50 Lactobacillus Ascusbbr_1686 SEQ ID PTA-124016, Coryne- Ascusbbr_226 SEQ ID PATENT201703003 (Genus) NO: 6 PTA-124039, bacterium NO: PATENT201703001, (Genus) 338 PATENT201703002, PATENT201703003, PATENT201703004, B-67270 Faecali- Ascusbbr_1789 SEQ ID PTA-124016, Streptococcus Ascusbbr_17 SEQ ID PATENT201703002, bacterium NO: 7 PTA-124039, (Genus) NO: PATENT201703003, (Genus) PATENT201703001 339 PATENT201703004 Lactobacillus Ascusbbr_3820 SEQ ID PTA-124039, Lactobacillus Ascusbbr_14690(A) SEQ ID PTA-124039, (Genus) NO: 8 PATENT201703002 (Genus) NO: PATENT201703001, 340 PATENT201703002, PATENT201703003, PATENT201703004 Lactobacillus Ascusbbr_14690(B) SEQ ID PTA-124016, (Genus) NO: 371 Lactobacillus Ascusbbr_14690(C) SEQ ID PATENT201703004 (Genus) NO: 372 Hydro- Ascusbbr_173 SEQ ID PTA-124016, Coryne- Ascusbbr_18 SEQ ID PATENT201703003 genoanaero NO: 9 PTA-124039 bacterium NO: bacterium (Genus) 341 (Genus) Peptostrepto- Ascusbbr_3089 SEQ ID PTA-124016 Peptostrepto- Ascusbbr_7363 SEQ ID PTA-124016 coccaceae NO: 10 coccaceae NO: Clostridium (Clostridium 342 Cluster XI Cluster XI) (Family + (Family + Cluster) Cluster) Acrocar- Ascusbbr_167 SEQ ID Coryne- Ascusbbr_35 SEQ ID PATENT201703002, pospora NO: 11 bacterium NO: PATENT201703003, (Genus) (Genus) 343 PATENT201703004 Lactobacillus Ascusbbr_301568 SEQ ID Coryne- Ascusbbr_7779 SEQ ID PATENT201703002, (Genus) NO: 12 bacterium NO: PATENT201703003, (Genus) 344 PATENT201703004 Bacillus Ascusbbr_33(A) SEQ ID PATENT201703002, Lachno- Ascusbbr_10593(A) SEQ ID PTA-124039, (Genus) NO: 13 PATENT201703003, spiraceae NO: PATENT201703001, B-67266 (Clostridium 345 PATENT201703002, Cluster XlVa) PATENT201703003 (Family + Cluster) Bacillus Ascusbbr_33(B) SEQ ID PATENT201703001, Lachno- Ascusbbr_10593(B) SEQ ID PTA-124016, (Genus) NO: spiraceae NO: 374 (Clostridium 381 Cluster XlVa) (Family + Cluster) Lactobacillus Ascusbbr_25200 SEQ ID PATENT201703001, Lachno- Ascusbbr_32731(A) SEQ ID PTA-124016, (Genus) NO: 14 PATENT201703002, spiracea NO: PATENT201703001, PATENT201703003, incertae sedis 346 PATENT201703002 PATENT201703004 (Genus) Lachno- Ascusbbr_32731(B) SEQ ID PTA-124039 spiracea NO: incertae sedis 382 (Genus) Subdoli- Ascusbbr_84 SEQ ID PTA-124039, Rumino- Ascusbbr_359892 SEQ ID PTA-124039 granulum NO: 15 PATENT201703003 coccaceae NO: (Genus) (Clostridium 347 Cluster III) (Family + Cluster) Subdoli- Ascusbbr_136 SEQ ID PTA-124016 Lactobacillus Ascusbbr_25721 SEQ ID granulum NO: 16 (Genus) NO: (Genus) 348 Lachno- Ascusbbr_128 SEQ ID PATENT201703004 Streptococcus Ascusbbr_72076 SEQ ID PTA-124039, spiraceae NO: 17 (Genus) NO: PATENT201703001, Clostridium 349 PATENT201703002, Cluster XIVa PATENT201703003, (Family + PATENT201703004 Cluster) Lactobacillus Ascusbbr_322104 SEQ ID PATENT201703001 Lachno- Ascusbbr_6097 SEQ ID PTA-124016, (Genus) NO: 18 spiraceae NO: PTA-124039, (Clostridium 350 PATENT201703002, Cluster XlVa) PATENT201703003, (Family + PATENT201703004 Cluster) Lactobacillus Ascusbbr_409(A) SEQ ID PTA-124039, Lactobacillus Ascusbbr_265 (A) SEQ ID PATENT201703001, (Genus) NO: 19 PATENT201703002, (Genus) NO: PATENT201703002 PATENT201703003, 351 Lactobacillus Ascusbbr_409(B) SEQ ID PATENT201703004 PATENT201703004 (Genus) NO: 375 Lactobacillus Ascusbbr_409(C) SEQ ID PATENT201703001 (Genus) NO: 376 Lactobacillus Ascusbbr_409(D) SEQ ID PATENT201703001 Lactobacillus Ascusbbr_265 (B) SEQ ID PATENT201703001, (Genus) NO: (Genus) NO: PATENT201703002, 377 385 PATENT201703004 Leuconostoc Ascusbbr_127 SEQ ID B-67265 Paracoccus Ascusbbr_323376 SEQ ID PATENT201703002 (Genus) NO: 20 (Genus) NO: 352 Lachno- Ascusbbr_14834 SEQ ID PTA-124016, Cellulo- Ascusbbr_36257 SEQ ID PTA-124039 spiracea NO: 21 PTA-124039, silyticum NO: incertae sedis PATENT201703001, (Genus) 353 (Genus) PATENT201703002, PATENT201703003 Lactobacillus Ascusbbr_331885(A) SEQ ID PTA-124039, Blautia Ascusbbr_6957 SEQ ID PTA-124039, (Genus) NO: 22 PATENT201703002, (Genus) NO: PATENT201703002, PATENT201703003, 354 PATENT201703003 B-67269 Lactobacillus Ascusbbr_331885(B) SEQ ID PATENT201703001 (Genus) NO: 378 Lactobacillus Ascusbbr_331885(C) SEQ ID PATENT201703004 (Genus) NO: 379 Anaerofilum Ascusbbr_31 SEQ ID PTA-124039, Coryne- Ascusbbr_38 SEQ ID PATENT201703003 (Genus) NO: 23 PATENT201703002 bacterium NO: (Genus) 355 Lachno- Ascusbbr_2307 SEQ ID PTA-124039 Lachno- Ascusbbr_13398 SEQ ID PTA-124039, spiracea NO: 24 spiracea NO: PATENT201703003 incertae sedis incertae sedis 356 (Genus) (Genus) Lachno- Ascusbbr_247(A) SEQ ID PTA-124039, Coryne- Ascusbbr_57 SEQ ID PATENT201703003 spiraceae NO: 25 PATENT201703004 bacterium NO: Clostridium (Genus) 357 Cluster XIVa (Family + Cluster) Lachno- Ascusbbr_247(B) SEQ ID PTA-124016 spiraceae NO: Clostridium 380 Cluster XIVa (Family + Cluster) Microbacterium Ascusbbr_19 SEQ ID PATENT201703001, Coryne- Ascusbbr_285160 SEQ ID PTA-124039, (Genus) NO: 26 B-67264 bacterium NO: PATENT201703001, (Genus) 358 PATENT201703002, PATENT201703003, PATENT201703004 Verrucosispora Ascusbbr_69 SEQ ID Ruminococcus Ascusbbr_37385 SEQ ID (Genus) NO: 27 (Genus) NO: 359 Anaerofilum Ascusbbr_94 SEQ ID PATENT201703001, Lactobacillus Ascusbbr_118124 SEQ ID PATENT201703001 (Genus) NO: 28 PATENT201703004 (Genus) NO: 360 Clostridium Ascusbbr_313454 SEQ ID PATENT201703003, Roseburia Ascusbbr_32592 SEQ ID PATENT201703002 sensu stricto NO: 29 PATENT201703004 (Genus) NO: (Genus) 361 Lactobacillus Ascusbbr_351000 SEQ ID Lachno- Ascusbbr_110856 SEQ ID PATENT201703004 (Genus) NO: 30 spiraceae NO: (Clostridium 362 Cluster XlVa) (Family + Cluster) Lactobacillus Ascusbbr_1436(A) SEQ ID PTA-124039, Lachno- Ascusbbr_185064 SEQ ID PTA-124039, (Genus) NO: 31 PATENT201703001, spiraceae NO: PATENT201703001, PATENT201703002, (Clostridium 363 PATENT201703002 PATENT201703003, Cluster XlVb) PATENT201703004 (Family + Cluster) Lactobacillus Ascusbbr_1436(B) SEQ ID PTA-124016 (Genus) NO: 383 Lachno- Ascusbbr_28 SEQ ID PTA-124016, Clostridium Ascusbbr _3315 SEQ ID spiraceae NO: 32 PTA-124039, sensu stricto NO: Clostridium PATENT201703002 (Genus) 364 Cluster XIVa (Family + Cluster) Blautia (Genus) Ascusbbr_144 SEQ ID PTA-124039, Bacteroides Ascusbbr_578 SEQ ID PTA-124039 NO: 33 PATENT201703002 dorei NO: 365 Lactobacillus Ascusbbr_42760(A) SEQ ID PTA-124039, Lactobacillus Ascusbbr_21169 SEQ ID PATENT201703001 (Genus) NO: 34 PATENT201703002, (Genus) NO: PATENT201703003, 366 PATENT201703004 Lactobacillus Ascusbbr_42760(B) SEQ ID PATENT201703001 (Genus) NO: 384 Lactobacillus Ascusbbr_134994 SEQ ID Lactobacillus Ascusbbr_48584 SEQ ID PATENT201703004 (Genus) NO: 35 (Genus) NO: 367 Lactobacillus Ascusbbr_358773 SEQ ID Nectriaceae Ascusfbr_15 SEQ ID (Genus) NO: 36 (Family) NO: 51 Pseudomonas Ascusbbr_2503 SEQ ID PATENT201703001 Filobasidium Ascusfbr _131 SEQ ID (Genus) NO: 37 floriforme NO: 52 (Genus + species) Sporobacter Ascusbbr_312 SEQ ID PATENT201703002 Gibberella Ascusfbr _26 SEQ ID (Genus) NO: 39 zeae (Genus NO: 53 + species) Lactobacillus Ascusbbr_140914 SEQ ID Alatospora Ascusfbr _2616 SEQ ID (Genus) NO: 40 (Genus) NO: 54 Lactobacillus Ascusbbr_257627 SEQ ID Hypocreaceae Ascusfbr _12 SEQ ID (Genus) NO: 41 (Family) NO: 55 Lactobacillus Ascusbbr_310088 SEQ ID Pichia Ascusfbr _53 SEQ ID (Genus) NO: 42 fermentans NO: 56 (Genus + species) Lachno- Ascusbbr_91 SEQ ID PTA-124016, Candida Ascusfbr _1379 SEQ ID spiracea NO: 43 PTA-124039, railenensis NO: 57 incertae sedis PATENT201703002, (Genus + (Genus) PATENT201703003 species) Lactobacillus Ascusbbr_150100 SEQ ID Hypocreaceae Ascusfbr _122 SEQ ID (Genus) NO: 44 (Family) NO: 58 Lactobacillus Ascusbbr_252028 SEQ ID Lactobacillus Ascusbbr_830 SEQ ID PTA-124039 (Genus) NO: 45 (Genus) NO: 368 Clostridium Ascusbbr_2676 SEQ ID PATENT201703003 Clostridium Ascusbbr_105932 SEQ ID PATENT201703001 beijerinckii NO: PATENT201703004 saccharo- NO: PATENT201703002 (Genus + 386 lyticum 387 species) (Genus + species)

TABLE 3 Bacteria of the present disclosure. Predicted Sequence Predicted Sequence Closest Taxa Identifier for Closest Taxa Identifier for of Isolated Strain Associated of Isolated Strain Associated Microbes Designation Marker Microbes Designation Marker 1. Clostridium XIVb (Cluster) Ascusbbr_6   SEQ ID Actinomyces (Genus) Ascusbbr_2226 SEQ ID NO: 59  NO: 199 2. Gemmiger (Genus) Ascusbbr_113  SEQ ID Succiniclasticum Ascusbbr_2227 SEQ ID NO: 60  (Genus) NO: 200 3. Lactobacillus (Genus) Ascusbbr_116  SEQ ID Beijerinckia (Genus) Ascusbbr_2229 SEQ ID NO: 61  NO: 201 4. Clostridium XI (Cluster) Ascusbbr_129  SEQ ID Bosea (Genus) Ascusbbr_2235 SEQ ID NO: 62  NO: 202 5. Jeotgalicoccus (Genus) Ascusbbr_265  SEQ ID Sporobacter (Genus) Ascusbbr_2237 SEQ ID NO: 63  NO: 203 6. Lactobacillus (Genus) Ascusbbr_275  SEQ ID Facklamia (Genus) Ascusbbr_2251 SEQ ID NO: 64  NO: 204 7. Lactobacillus (Genus) Ascusbbr_343  SEQ ID Acinetobacter (Genus) Ascusbbr_2266 SEQ ID NO: 65  NO: 205 8. Lactobacillus (Genus) Ascusbbr_363  SEQ ID Brevundimonas (Genus) Ascusbbr_2284 SEQ ID NO: 66  NO: 206 9. Jeotgalicoccus (Genus) Ascusbbr_399  SEQ ID Ochrobactrum (Genus) Ascusbbr_2285 SEQ ID NO: 67  NO: 207 10. Lactobacillus (Genus) Ascusbbr_444  SEQ ID Alcaligenes (Genus) Ascusbbr_2290 SEQ ID NO: 68  NO: 208 11. Jeotgalicoccus (Genus) Ascusbbr_498  SEQ ID Pseudochrobactrum Ascusbbr_2291 SEQ ID NO: 69  (Genus) NO: 209 12. Lactobacillus (Genus) Ascusbbr_542  SEQ ID Jeotgalicoccus (Genus) Ascusbbr_2292 SEQ ID NO: 70  NO: 210 13. Lactobacillus (Genus) Ascusbbr_561  SEQ ID Jeotgalicoccus (Genus) Ascusbbr_2293 SEQ ID NO: 71  NO: 211 14. Lactobacillus (Genus) Ascusbbr_570  SEQ ID Acinetobacter (Genus) Ascusbbr_2294 SEQ ID NO: 72  NO: 212 15. Corynebacterium (Genus) Ascusbbr_616  SEQ ID Sphingobacterium Ascusbbr_2295 SEQ ID NO: 73  (Genus) NO: 213 16. Microbacterium (Genus) Ascusbbr_620  SEQ ID Lachnospiracea (Genus) Ascusbbr_2301 SEQ ID NO: 74  NO: 214 17. Jeotgalicoccus (Genus) Ascusbbr_690  SEQ ID Azospirillum (Genus) Ascusbbr_2302 SEQ ID NO: 75  NO: 215 18. Jeotgalicoccus (Genus) Ascusbbr_705  SEQ ID Lactobacillus (Genus) Ascusbbr_2313 SEQ ID NO: 76  NO: 216 19. Glycomyces (Genus) Ascusbbr_793  SEQ ID Clavibacter (Genus) Ascusbbr_2320 SEQ ID NO: 77  NO: 217 20. Streptomyces (Genus) Ascusbbr_795  SEQ ID Clostridium XIVa Ascusbbr_2324 SEQ ID NO: 78  (Cluster) NO: 218 21. Saccharopolyspora (Genus) Ascusbbr_796  SEQ ID Clostridium XIVa Ascusbbr_2325 SEQ ID NO: 79  (Cluster) NO: 219 22. Brevibacterium (Genus) Ascusbbr_803  SEQ ID Lactobacillus (Genus) Ascusbbr_2328 SEQ ID NO: 80  NO: 220 23. Microbacterium (Genus) Ascusbbr_804  SEQ ID Clostridium XIVa Ascusbbr_2331 SEQ ID NO: 81  (Cluster) NO: 221 24. Acinetobacter (Genus) Ascusbbr_840  SEQ ID Bacillus (Genus) Ascusbbr_2337 SEQ ID NO: 82  NO: 222 25. Lactococcus (Genus) Ascusbbr_846  SEQ ID Methanoplanus (Genus) Ascusbbr_2354 SEQ ID NO: 83  NO: 223 26. Cloacibacterium (Genus) Ascusbbr_867  SEQ ID Mogibacterium (Genus) Ascusbbr_2361 SEQ ID NO: 84  NO: 224 27. Mycobacterium (Genus) Ascusbbr_929  SEQ ID Brachybacterium Ascusbbr_2368 SEQ ID NO: 85  (Genus) NO: 225 28. Leucobacter (Genus) Ascusbbr_944  SEQ ID Facklamia (Genus) Ascusbbr_2376 SEQ ID NO: 86  NO: 226 29. Lactobacillus (Genus) Ascusbbr_950  SEQ ID Clostridium XIVa Ascusbbr_2378 SEQ ID NO: 87  (Cluster) NO: 227 30. Rothia (Genus) Ascusbbr_951  SEQ ID Clostridium XIVa Ascusbbr_2380 SEQ ID NO: 88  (Cluster) NO: 228 31. Lactobacillus (Genus) Ascusbbr_996  SEQ ID Syntrophomonas Ascusbbr_2383 SEQ ID NO: 89  (Genus) NO: 229 32. Clavibacter (Genus) Ascusbbr_1005 SEQ ID Beijerinckia (Genus) Ascusbbr_2386 SEQ ID NO: 90  NO: 230 33. Hydrogenoanaerobacterium Ascusbbr_1029 SEQ ID Lactobacillus (Genus) Ascusbbr_2390 SEQ ID (Genus) NO: 91  NO: 231 34. Howardella (Genus) Ascusbbr_1036 SEQ ID Lactobacillus (Genus) Ascusbbr_2391 SEQ ID NO: 92  NO: 232 35. Clostridium (Genus) Ascusbbr_1069 SEQ ID Lactobacillus (Genus) Ascusbbr_2395 SEQ ID NO: 93  NO: 233 36. Ascusbbr_1128 SEQ ID Erysipelotrichaceae Ascusbbr_2397 SEQ ID NO: 94  (Family) NO: 234 37. Hydrogenoanaerobacterium Ascusbbr_1139 SEQ ID Rummeliibacillus Ascusbbr_2399 SEQ ID (Genus) NO: 95  (Genus) NO: 235 38. Papillibacter (Genus) Ascusbbr_1169 SEQ ID Acinetobacter (Genus) Ascusbbr_2402 SEQ ID NO: 96  NO: 236 39. Butyricicoccus (Genus) Ascusbbr_1185 SEQ ID Lactococcus (Genus) Ascusbbr_2403 SEQ ID NO: 97  NO: 237 40. Eubacterium (Genus) Ascusbbr_1245 SEQ ID Propionibacterium Ascusbbr_2412 SEQ ID NO: 98  (Genus) NO: 238 41. Turicibacter (Genus) Ascusbbr_1258 SEQ ID Clostridium (Genus) Ascusbbr_2413 SEQ ID NO: 99  NO: 239 42. Lactobacillus (Genus) Ascusbbr_1264 SEQ ID Clostridium XIVa Ascusbbr_2416 SEQ ID NO: 100 (Cluster) NO: 240 43. Asaccharobacter (Genus) Ascusbbr_1332 SEQ ID Rummeliibacillus Ascusbbr_2419 SEQ ID NO: 101 (Genus) NO: 241 44. Faecalibacterium (Genus) Ascusbbr_1360 SEQ ID Ralstonia (Genus) Ascusbbr_2420 SEQ ID NO: 102 NO: 242 45. Clostridium XIVa (Cluster) Ascusbbr_1363 SEQ ID Brachybacterium Ascusbbr_2421 SEQ ID NO: 103 (Genus) NO: 243 46. Clostridium XIVa (Cluster) Ascusbbr_1422 SEQ ID Ruminobacter (Genus) Ascusbbr_2423 SEQ ID NO: 104 NO: 244 47. Clostridium IV (Cluster) Ascusbbr_1424 SEQ ID Glycomyces (Genus) Ascusbbr_2427 SEQ ID NO: 105 NO: 245 48. Clostridium XIVb (Cluster) Ascusbbr_1433 SEQ ID Psychrobacter (Genus) Ascusbbr_2428 SEQ ID NO: 106 NO: 246 49. Butyricicoccus (Genus) Ascusbbr_1456 SEQ ID Yaniella (Genus) Ascusbbr_2429 SEQ ID NO: 107 NO: 247 50. Sporobacter (Genus) Ascusbbr_1485 SEQ ID Clostridium IV (Cluster) Ascusbbr_2431 SEQ ID NO: 108 NO: 248 51. Butyricicoccus (Genus) Ascusbbr_1488 SEQ ID Clostridium (Genus) Ascusbbr_2434 SEQ ID NO: 109 NO: 249 52. Hydrogenoanaerobacterium Ascusbbr_1490 SEQ ID Clostridium XIVa Ascusbbr_2435 SEQ ID (Genus) NO: 110 (Cluster) NO: 250 53. Anaerofilum (Genus) Ascusbbr_1493 SEQ ID Clostridium (Genus) Ascusbbr_2436 SEQ ID NO: 111 NO: 251 54. Clostridium XIVa (Cluster) Ascusbbr_1536 SEQ ID Clostridium XIVa Ascusbbr_2437 SEQ ID NO: 112 (Cluster) NO: 252 55. Clostridium XIVa (Cluster) Ascusbbr_1541 SEQ ID Cohnella (Genus) Ascusbbr_2438 SEQ ID NO: 113 NO: 253 56. Lachnospiracea (Family) Ascusbbr_1572 SEQ ID Chthonomonas (Genus) Ascusbbr_2441 SEQ ID NO: 114 NO: 254 57. Lachnospiracea (Family) Ascusbbr_1592 SEQ ID Streptophyta Ascusbbr_2445 SEQ ID NO: 115 (Unranked Clade) NO: 255 58. Butyricicoccus (Genus) Ascusbbr_1611 SEQ ID Acinetobacter (Genus) Ascusbbr_2452 SEQ ID NO: 116 NO: 256 59. Pediococcus (Genus) Ascusbbr_1614 S EQ ID Clostridium XIVb Ascusbbr_2456 SEQ ID NO: 117 NO: 257 60. Acetanaerobacterium (Genus) Ascusbbr_1616 SEQ ID Neisseria Ascusbbr_2465 SEQ ID NO: 118 NO: 258 61. Hydrogenoanaerobacterium Ascusbbr_1623 SEQ ID Butyricicoccus Ascusbbr_2471 SEQ ID (Genus) NO: 119 NO: 259 62. Butyricicoccus (Genus) Ascusbbr_1625 SEQ ID Sporobacter Ascusbbr_2472 SEQ ID NO: 120 NO: 260 63. Lachnospiracea (Family) Ascusbbr_1632 SEQ ID Sporobacter Ascusbbr_2476 SEQ ID NO: 121 NO: 261 64. Erysipelotrichaceae (Family) Ascusbbr_1634 SEQ ID Syntrophomonas Ascusbbr_2477 SEQ ID NO: 122 NO: 262 65. Lachnospiracea (Family) Ascusbbr_1635 SEQ ID Desulfotomaculum Ascusbbr_2478 SEQ ID NO: 123 NO: 263 66. Butyricicoccus (Genus) Ascusbbr_1646 SEQ ID Streptophyta Ascusbbr_2482 SEQ ID NO: 124 NO: 264 67. Butyricicoccus (Genus) Ascusbbr_1669 SEQ ID Acetomicrobium Ascusbbr_2489 SEQ ID NO: 125 NO: 265 68. Butyricicoccus (Genus) Ascusbbr_1670 SEQ ID Acinetobacter Ascusbbr_2492 SEQ ID NO: 126 NO: 266 69. Butyricicoccus (Genus) Ascusbbr_1674 SEQ ID Erysipelotrichaceae Ascusbbr_2493 SEQ ID NO: 127 NO: 267 70. Butyricicoccus (Genus) Ascusbbr_1678 SEQ ID Jeotgalicoccus Ascusbbr_2496 SEQ ID NO: 128 NO: 268 71. Lachnospiracea (Family) Ascusbbr_1679 SEQ ID Selenomonas Ascusbbr_2497 SEQ ID NO: 129 NO: 269 72. Howardella (Genu) Ascusbbr_1684 SEQ ID Howardella Ascusbbr_2498 SEQ ID NO: 130 NO: 270 73. Lachnospiracea (Family) Ascusbbr_1685 SEQ ID Clostridium XIVa Ascusbbr_2500 SEQ ID NO: 131 NO: 271 74. Clavibacter (Genus) Ascusbbr_1694 SEQ ID Lachnospiracea Ascusbbr_2501 SEQ ID NO: 132 NO: 272 75. Butyricicoccus (Genus) Ascusbbr_1695 SEQ ID Lachnospiracea Ascusbbr_2504 SEQ ID NO: 133 NO: 273 76. Hydrogenoanaerobacterium Ascusbbr_1715 SEQ ID Clostridium XIVa Ascusbbr_2506 SEQ. ID (Genus) NO: 134 NO: 274 77. Spiroplasma (Genus) Ascusbbr_1720 SEQ ID Lachnospiracea Ascusbbr_2508 SEQ ID NO: 135 NO: 275 78. Clostridium XIVa (Cluster) Ascusbbr_1722 SEQ ID Bacillus Ascusbbr_2509 SEQ ID NO: 136 NO: 276 79. Jeotgalicoccus (Genus) Ascusbbr_1723 SEQ ID Paenibacillus Ascusbbr_2510 SEQ ID NO: 137 NO: 277 80. Syntrophomonas (Genus) Ascusbbr_1743 SEQ ID Eubacterium Ascusbbr_2511 SEQ ID NO: 138 NO: 278 81. Clostridium IV (Cluster) Ascusbbr_1746 SEQ ID Amphibacillus Ascusbbr_2512 SEQ ID NO: 139 NO: 279 82. Lachnospiracea (Family) Ascusbbr_1748 SEQ ID Staphylococcus Ascusbbr_2513 SEQ ID NO: 140 NO: 280 83. Hydrogenoanaerobacterium Ascusbbr_1753 SEQ ID Paenibacillus Ascusbbr_2514 SEQ ID (Genus) NO: 141 NO: 281 84. Oscillibacter (Genus) Ascusbbr_1756 SEQ ID Clostridium IV Ascusbbr_2515 SEQ ID NO: 142 NO: 282 85. Clostridium IV (Cluster) Ascusbbr_1785 SEQ ID Prevotella Ascusbbr_2516 SEQ ID NO: 143 NO: 283 86. Sporobacter (Genus) Ascusbbr_1812 SEQ ID Barnesiella Ascusbbr_2518 SEQ ID NO: 144 NO: 284 87. Pediococcus (Genus) Ascusbbr_1821 SEQ ID Clostridium XIVa Ascusbbr_2519 SEQ ID NO: 145 NO: 285 88. Sporobacter (Genus) Ascusbbr_1824 SEQ ID Clostridium XIVa Ascusbbr_2520 SEQ ID NO: 146 NO: 286 89. Bacillus (Genus) Ascusbbr_1866 SEQ ID Sharpea Ascusbbr_2521 SEQ ID NO: 147 NO: 287 90. Cellulomonas (Genus) Ascusbbr_1882 SEQ ID Lachnospiracea Ascusbbr_2522 SEQ ID NO: 148 NO: 288 91. Syntrophomonas (Genus) Ascusbbr_1887 SEQ ID Leucobacter Ascusbbr_2523 SEQ ID NO: 149 NO: 289 92. Cryptanaerobacter (Genus) Ascusbbr_1928 SEQ ID Lactonifactor Ascusbbr_2524 SEQ ID NO: 150 NO: 290 93. Sporobacter (Genus) Ascusbbr_1932 SEQ ID Lachnospiracea Ascusbbr_2525 SEQ ID NO: 151 NO: 291 94. Hydrogenoanaerobacterium Ascusbbr_1933 SEQ ID Succiniclasticum Ascusbbr_2526 SEQ ID (Genus) NO: 152 NO: 292 95. Clostridium IV (Cluster) Ascusbbr_1937 SEQ ID Acidovorox Ascusbbr_2528 SEQ ID NO: 153 NO: 293 96. Hydrogenoanaerobacterium Ascusbbr_1953 SEQ ID Acinetobacter Ascusbbr_2530 SEQ ID (Genus) NO: 154 NO: 294 97. Spiroplasma (Genus) Ascusbbr_1955 SEQ ID Comamonas Ascusbbr_2531 SEQ ID NO: 155 NO: 295 98. Erysipelotrichaceae (Family) Ascusbbr_1956 SEQ ID Prevotella Ascusbbr_2533 SEQ ID NO: 156 NO: 296 99. Pseudgflavonffractor (Genus) Ascusbbr_1957 SEQ ID Clostridium IV Ascusbbr_2534 SEQ ID NO: 157 NO: 297 100. Clostridium XIVa (Cluster) Ascusbbr_1967 SEQ ID Clostridium Ascusbbr_2535 SEQ ID NO: 158 NO: 298 101. Mogibacterium (Genus) Ascusbbr_1969 SEQ ID Succiniclasticum Ascusbbr_2536 SEQ ID NO: 159 NO: 299 102. Clostridium (Genus) Ascusbbr_1973 SEQ ID Lachnospiracea Ascusbbr_2538 SEQ ID NO: 160 NO: 300 103. Clostridium IV (Cluster) Ascusbbr_2020 SEQ ID Pedobacter Ascusbbr_2539 SEQ ID NO: 161 NO: 301 104. Citrobacter (Genus) Ascusbbr_2023 SEQ ID Clostridium XII Ascusbbr_2540 SEQ ID NO: 162 NO: 302 105. Hydrogenoanaerobacterium Ascusbbr_2033 SEQ ID Flavobacterium Ascusbbr_2544 SEQ ID (Genus) NO: 163 NO: 303 106. Clostridium XIVa (Cluster) Ascusbbr_2047 SEQ ID Clostridium Ascusbbr_2545 SEQ ID NO: 164 NO: 304 107. Clostridium XIVa (Cluster) Ascusbbr_2049 SEQ ID Alkaliphilus Ascusbbr_2547 SEQ ID NO: 165 NO: 305 108. Clostridium (Genus) Ascusbbr_2057 SEQ ID Arthrobacter Ascusbbr_2548 SEQ ID NO: 166 NO: 306 109. Erysipelotrichaceae (Family) Ascusbbr_2069 SEQ ID Flavobacterium Ascusbbr_2549 SEQ ID NO: 167 NO: 307 110. Clostridium XIVb (Cluster) Ascusbbr_2073 SEQ ID Roseburia Ascusbbr_2550 SEQ ID NO: 168 NO: 308 111. Clostridium XIVb (Cluster) Ascusbbr_2076 SEQ ID Paenibacillus Ascusbbr_2551 SEQ ID NO: 169 NO: 309 112. Butyricicoccus (Genus) Ascusbbr_2101 SEQ ID Olivibacter Ascusbbr_2553 SEQ ID NO: 170 NO: 310 113. Pediococcus (Genus) Ascusbbr_2118 SEQ ID Clostridium XII Ascusbbr_2554 SEQ ID NO: 171 NO: 311 114. Sphingomonas (Genus) Ascusbbr_2127 S EQ ID Sphingobacterium Ascusbbr_2555 SEQ. ID NO: 172 NO: 312 115. Clostridium XIVa (Cluster) Ascusbbr_2131 SEQ ID Sphingobacterium Ascusbbr_2556 SEQ ID NO: 173 NO: 313 116. Clostridium IV (Cluster) Ascusbbr_2132 SEQ ID Anaerosporobacter Ascusbbr_2557 SEQ ID NO: 174 NO: 314 117. Clostridium XIVb (Cluster) Ascusbbr_2136 SEQ ID Clostridium XII Ascusbbr_2560 SEQ ID NO: 175 NO: 315 118. Clostridium XIVb (Cluster) Ascusbbr_2137 SEQ ID Clostridium XII Ascusbbr_2561 SEQ ID NO: 176 NO: 316 119. Methylobacterium (Genus) Ascusbbr_2149 SEQ ID Clostridium Ascusbbr_2562 SEQ ID NO: 177 NO: 317 120. Salana (Genus) Ascusbbr_2177 S EQ ID Pedobacter Ascusbbr_2563 SEQ. ID NO: 178 NO: 318 121. Petrobacter (Genus) Ascusbbr_2178 SEQ ID Bacillus Ascusbbr_2564 SEQ. ID NO: 179 NO: 319 122. Bacillus (Genus) Ascusbbr_2180 SEQ ID Paenibacillus Ascusbbr_2565 SEQ. ID NO: 180 NO: 320 123. Thermovibrio (Genus) Ascusbbr_2183 SEQ ID Prevotella Ascusbbr_2566 SEQ. ID NO: 181 NO: 321 124. Erysipelotrichaceae (Family) Ascusbbr_2184 SEQ ID Lachnospiracea (Family) Ascusbbr_2567 SEQ. ID NO: 182 NO: 322 125. Selenomonas (Genus) Ascusbbr_2192 SEQ ID Lachnospiracea (Family) Ascusbbr_2568 SEQ ID NO: 183 NO: 323 126. Glaciecola (Genus) Ascusbbr_2193 SEQ ID Escherichia/Shigella Ascusbbr_2594 SEQ ID NO: 184 (Genus) NO: 324 127. Lactobacillus (Genus) Ascusbbr_2195 SEQ ID Lactobacillus (Genus) Ascusbbr_2603 SEQ ID NO: 185 NO: 325 128. Eubacterium (Genus) Ascusbbr_2200 SEQ ID Corynebacterium (Genus) Ascusbbr_2605 SEQ ID NO: 186 NO: 326 129. Thermomicrobium (Genus) Ascusbbr_2201 SEQ ID Lactobacillus (Genus) Ascusbbr_2615 SEQ ID NO: 187 NO: 327 130. Acidobacteria (Genus) Ascusbbr_2204 SEQ ID Lactobacillus (Genus) Ascusbbr_2625 SEQ ID NO: 188 NO: 328 131. Chlorobaculum (Genus) Ascusbbr_2205 SEQ ID Escherichia/Shigella Ascusbbr_2640 SEQ ID NO: 189 (Genus) NO: 329 132. Rothia (Genus) Ascusbbr_2208 SEQ ID Lactobacillus (Genus) Ascusbbr_2644 SEQ ID NO: 190 NO: 330 133. Selenomonas (Genus) Ascusbbr_2210 SEQ ID Lactobacillus (Genus) Ascusbbr_2665 SEQ ID NO: 191 NO: 331 134. Clostridium XIVa (Cluster) Ascusbbr_2215 SEQ ID Lactobacillus (Genus) Ascusbbr_2684 SEQ ID NO: 192 NO: 332 135. Virgibacillus (Genus) Ascusbbr_2216 SEQ ID Lactobacillus (Genus) Ascusbbr_2694 SEQ ID NO: 193 NO: 333 136. Sphingomonas (Genus) Ascusbbr_2218 SEQ ID Lactobacillus (Genus) Ascusbbr_2699 SEQ ID NO: 194 NO: 334 137. Citricoccus (Genus) Ascusbbr_2219 SEQ ID Lactobacillus (Genus) Ascusbbr_2709 SEQ ID NO: 195 NO: 335 138. Catenibacterium (Genus) Ascusbbr_2220 SEQ ID Lactobacillus (Genus) Ascusbbr_2710 SEQ ID NO: 196 NO: 336 139. Amycolatopsis (Genus) Ascusbbr_2224 SEQ ID Enterococcus (Genus) Ascusbbr_2714 SEQ ID NO: 197 NO: 337 140. Sphingobium (Genus) Ascusbbr_2225 SEQ. ID Clostridium sensustricto Ascusbbr_2676 SEQ. ID NO: 198 (Genus) NO: 386 141. Clostridium_XIVa (Cluster)  Ascusbbr_105932 SEQ. ID NO: 387

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 shows a general workflow of one embodiment of the method for determining the absolute abundance of one or more active microorganism strains.

FIG. 2 shows a general workflow of one embodiment of a method for determining the co-occurrence of one or more, or two or more, active microorganism strains in a sample with one or more metadata (environmental) parameters, followed by leveraging cluster analysis and community detection methods on the network of determined relationships.

FIG. 3 is a cartoon depiction of an exemplary chicken's anatomy.

FIG. 4 is an image of a dissected gastrointestinal track of a chicken from the beak to the cloaca.

FIG. 5 depicts the complex microbial interactions occurring in the gastrointestinal tract. A well-balanced commensal microbial load is involved in maintaining multiple homeostatic systems.

FIG. 6 depicts the likely results of a lectin binding assay with isolated microbial strains and a mannose-binding lectin (MBL).

FIG. 7 depicts the likely results of a gelatin/collagen binding assay with isolated microbial strains. CP=Clostridium perfringens, Strain 1=avirulent cnaA positive, Strain 2=avirulent cnaA negative. All reported results were corrected by their respective controls

FIG. 8 depicts a histogram the rate of microbial convergence across the experimental groups.

FIG. 9 depicts a histogram of the final percentage mortality for the experiment.

DETAILED DESCRIPTION Definitions

While the following terms are believed to be well understood by one of ordinary skill in the art, the following definitions are set forth to facilitate explanation of the presently disclosed subject matter.

The term “a” or “an” may refer to one or more of that entity, i.e. can refer to plural referents. As such, the terms “a” or “an”, “one or more” and “at least one” are used interchangeably herein. In addition, reference to “an element” by the indefinite article “a” or “an” does not exclude the possibility that more than one of the elements is present, unless the context clearly requires that there is one and only one of the elements.

Reference throughout this specification to “one embodiment”, “an embodiment”, “one aspect”, or “an aspect” means that a particular feature, structure or characteristic described in connection with the embodiment is included in at least one embodiment of the present disclosure. Thus, the appearances of the phrases “in one embodiment” or “in an embodiment” in various places throughout this specification are not necessarily all referring to the same embodiment. Furthermore, the particular features, structures, or characteristics can be combined in any suitable manner in one or more embodiments.

As used herein, in particular embodiments, the terms “about” or “approximately” when preceding a numerical value indicates the value plus or minus a range of 10%.

As used herein the terms “microorganism” or “microbe” should be taken broadly. These terms are used interchangeably and include, but are not limited to, the two prokaryotic domains, Bacteria and Archaea, eukaryotic fungi and protists, as well as viruses. In some embodiments, the disclosure refers to the “microbes” of Table 1 and/or Table 3, or the “microbes” incorporated by reference. This characterization can refer to not only the predicted taxonomic microbial identifiers of the table, but also the identified strains of the microbes listed in the table.

The term “bioensemble,” “microbial ensemble,” or “synthetic ensemble” refers to a composition comprising one or more active microbes identified by methods, systems, and/or apparatuses of the present disclosure and that do not naturally exist in a naturally occurring environment and/or at ratios or amounts that do not exist in nature. A bioensemble is a subset of a microbial community of individual microbial species, or strains of a species, which can be described as carrying out a common function, or can be described as participating in, or leading to, or correlating with, a recognizable parameter, such as a phenotypic trait of interest (e.g. increased feed efficiency in poultry). The bioensemble may comprise two or more species, or strains of a species, of microbes. In some instances, the microbes coexist within the community symbiotically.

In certain aspects of the disclosure, bioensembles are or are based on one or more isolated microbes that exist as isolated and biologically pure cultures. It will be appreciated by one of ordinary skill in the art that an isolated and biologically pure culture of a particular microbe, denotes that said culture is substantially free (within scientific reason) of other living organisms and contains only the individual microbe in question. The culture can contain varying concentrations of said microbe. The present disclosure notes that isolated and biologically pure microbes often “necessarily differ from less pure or impure materials.” See, e.g. In re Bergstrom, 427 F.2d 1394, (CCPA 1970) (discussing purified prostaglandins), see also, In re Bergy, 596 F.2d 952 (CCPA 1979) (discussing purified microbes), see also, Parke-Davis & Co. v. H. K. Mulford & Co., 189 F. 95 (S.D.N.Y. 1911) (J. Hand discussing purified adrenaline, aff'd in part, rev'd in part, 196 F. 496 (2d Cir. 1912), each of which are incorporated herein by reference. Furthermore, in some aspects, implementation of the disclosure can require certain quantitative measures of the concentration or purity limitations that must be achieved for an isolated and biologically pure microbial culture to be used in the disclosed microbial ensembles. The presence of these purifty values, in certain embodiments, is a further attribute that distinguishes the microbes identified by the presently disclosed method from those microbes existing in a natural state. See, e.g., Merck & Co. v. Olin Mathieson Chemical Corp., 253 F.2d 156 (4^(th) Cir. 1958) (discussing purity limitations for vitamin B12 produced by microbes), incorporated herein by reference.

Bioensembles can be applied or administered to a target, such as a target environment, population, individual, animal, and/or the like.

The term “microbial community” means a group of microbes comprising two or more species or strains. Unlike bioensembles, a microbial community does not have to be carrying out a common function, or does not have to be participating in, or leading to, or correlating with, a recognizable parameter, such as a phenotypic trait of interest (e.g. increased feed efficiency in poultry).

As used herein, “isolate,” “isolated,” “isolated microbe,” and like terms, are intended to mean that the one or more microorganisms has been separated from at least one of the materials with which it is associated in a particular environment (for example soil, water, animal tissue).

Microbes of the present disclosure may include spores and/or vegetative cells. In some embodiments, microbes of the present disclosure include microbes in a viable but non-culturable (VBNC) state, or a quiescent state. See Liao and Zhao (US Publication US2015267163A1). In some embodiments, microbes of the present disclosure include microbes in a biofilm. See Merritt et al. (U.S. Pat. No. 7,427,408).

Thus, an “isolated microbe” does not exist in its naturally occurring environment; rather, it is through the various techniques described herein that the microbe has been removed from its natural setting and placed into a non-naturally occurring state of existence. Thus, the isolated strain or isolated microbe may exist as, for example, a biologically pure culture, or as spores (or other forms of the strain) in association with an acceptable carrier.

As used herein, “spore” or “spores” refer to structures produced by bacteria and fungi that are adapted for survival and dispersal. Spores are generally characterized as dormant structures; however, spores are capable of differentiation through the process of germination. Germination is the differentiation of spores into vegetative cells that are capable of metabolic activity, growth, and reproduction. The germination of a single spore results in a single fungal or bacterial vegetative cell. Fungal spores are units of asexual reproduction, and in some cases are necessary structures in fungal life cycles. Bacterial spores are structures for surviving conditions that may ordinarily be nonconductive to the survival or growth of vegetative cells.

As used herein, “microbial composition” refers to a composition comprising one or more microbes of the present disclosure, wherein a microbial composition, in some embodiments, is administered to animals of the present disclosure.

As used herein, “carrier”, “acceptable carrier”, or “pharmaceutical carrier” refers to a diluent, adjuvant, excipient, or vehicle with which the compound is administered. Such carriers can be sterile liquids, such as water and oils, including those of petroleum, animal, vegetable, or synthetic origin; such as peanut oil, soybean oil, mineral oil, sesame oil, and the like. Water or aqueous solution saline solutions and aqueous dextrose and glycerol solutions are preferably employed as carriers, in some embodiments as injectable solutions. In some embodiments, gelling agents are employed as carriers. Alternatively, the carrier can be a solid dosage form carrier, including but not limited to one or more of a binder (for compressed pills), a glidant, an encapsulating agent, a flavorant, and a colorant. The choice of carrier can be selected with regard to the intended route of administration and standard pharmaceutical practice. See Hardee and Baggo (1998. Development and Formulation of Veterinary Dosage Forms. 2^(nd) Ed. CRC Press. 504 pg.); E. W. Martin (1970. Remington's Pharmaceutical Sciences. 17^(th) Ed. Mack Pub. Co.); and Blaser et al. (US Publication US20110280840A1).

In some aspects, carriers may be granular in structure, such as sand or sand particles. In further aspects, the carriers may be dry, as opposed to a moist or wet carrier. In some aspects, carriers can be nutrititve substances and/or prebiotic substances selected from fructo-oligosaccharides, inulins, isomalto-oligosaccharides, lactitol, lactosucruse, lactulose, pyrodextrines, soy oligosaccharides, transgalacto-oligosaccharides, xylo-oligosaccharides, trace minerals, and vitamins. In some aspects, carriers can be in solid or liquid form. In some aspects, carriers can be zeolites, calcium carbonate, magnesium carbonate, silicon dioxide, ground corn, trehalose, chitosan, shellac, albumin, starch, skim-milk powder, sweet-whey powder, maltodextrin, lactose, and inulin. In some aspects, a carrier is water or physiological saline.

In certain aspects of the disclosure, the isolated microbes exist as isolated and biologically pure cultures. It will be appreciated by one of skill in the art, that an isolated and biologically pure culture of a particular microbe, denotes that said culture is substantially free (within scientific reason) of other living organisms and contains only the individual microbe in question. The culture can contain varying concentrations of said microbe. The present disclosure notes that isolated and biologically pure microbes often “necessarily differ from less pure or impure materials.” See, e.g. In re Bergstrom, 427 F.2d 1394, (CCPA 1970)(discussing purified prostaglandins), see also, In re Bergy, 596 F.2d 952 (CCPA 1979)(discussing purified microbes), see also, Parke-Davis & Co. v. H.K. Mulford & Co., 189 F. 95 (S.D.N.Y. 1911) (Learned Hand discussing purified adrenaline), aff'd in part, rev'd in part, 196 F. 496 (2d Cir. 1912), each of which are incorporated herein by reference. Furthermore, in some aspects, the disclosure provides for certain quantitative measures of the concentration, or purity limitations, that must be found within an isolated and biologically pure microbial culture. The presence of these purity values, in certain embodiments, is a further attribute that distinguishes the presently disclosed microbes from those microbes existing in a natural state. See, e.g., Merck & Co. v. Olin Mathieson Chemical Corp., 253 F.2d 156 (4th Cir. 1958) (discussing purity limitations for vitamin B12 produced by microbes), incorporated herein by reference.

As used herein, “individual isolates” should be taken to mean a composition, or culture, comprising a predominance of a single genera, species, or strain, of microorganism, following separation from one or more other microorganisms. The phrase should not be taken to indicate the extent to which the microorganism has been isolated or purified. However, “individual isolates” can comprise substantially only one genus, species, or strain, of microorganism.

As used herein, “microbiome” refers to the collection of microorganisms that inhabit the reproductive tract, integument system, digestive tract or gastrointestinal tract of an animal and the microorganisms' physical environment (i.e., the microbiome has a biotic and physical component). The microbiome is fluid and may be modulated by numerous naturally occurring and artificial conditions (e.g., change in diet, disease, antimicrobial agents, influx of additional microorganisms, etc.). The modulation of the gastrointestinal microbiome can be achieved via administration of the compositions of the disclosure can take the form of: (a) increasing or decreasing a particular Family, Genus, Species, or functional grouping of a microbe (i.e., alteration of the biotic component of the gastrointestinal microbiome) and/or (b) increasing or decreasing gastrointestinal pH, increasing or decreasing volatile fatty acids in the gastrointestinal tract, increasing or decreasing any other physical parameter important for gastrointestinal health (i.e., alteration of the abiotic component of the gut microbiome).

As used herein, “probiotic” refers to a substantially pure microbe (i.e., a single isolate) or a mixture of desired microbes, and may also include any additional components that can be administered to poultry for restoring microbiota. Probiotics or microbial inoculant compositions of the invention may be administered with an agent to allow the microbes to survive the environment of the gastrointestinal tract, i.e., to resist low pH and to grow in the gastrointestinal environment. In some embodiments, the present compositions (e.g., microbial compositions) are probiotics in some aspects.

As used herein, “prebiotic” refers to an agent that increases the number and/or activity of one or more desired microbes. Non-limiting examples of prebiotics that may be useful in the methods of the present disclosure include fructooligosaccharides (e.g., oligofructose, inulin, inulin-type fructans), galactooligosaccharides, amino acids, alcohols, isomalto-oligosaccharides, lactitol, lactosucruse, lactulose, pyrodextrines, soy oligosaccharides, transgalacto-oligosaccharides, xylo-oligosaccharides, vitamins, and mixtures thereof. See Ramirez-Farias et al. (2008. Br. J. Nutr. 4:1-10) and Pool-Zobel and Sauer (2007. J. Nutr. 137:2580-2584 and supplemental).

The term “growth medium” as used herein, is any medium which is suitable to support growth of a microbe. By way of example, the media may be natural or artificial including gastrin supplemental agar, LB media, blood serum, and tissue culture gels. It should be appreciated that the media may be used alone or in combination with one or more other media. It may also be used with or without the addition of exogenous nutrients.

The medium may be amended or enriched with additional compounds or components, for example, a component which may assist in the interaction and/or selection of specific groups of microorganisms. For example, antibiotics (such as penicillin) or sterilants (for example, quaternary ammonium salts and oxidizing agents) could be present and/or the physical conditions (such as salinity, nutrients (for example organic and inorganic minerals (such as phosphorus, nitrogenous salts, ammonia, potassium and micronutrients such as cobalt and magnesium), pH, and/or temperature) could be amended.

As used herein, the term “fowl” and “poultry” are used interchangeably to include both domesticated and non-domesticated birds belonging to the orders of Galliformes and Anseriformes. Fowl include chickens (broilers/fryers/roasters/capons/roosters/stewing hens), turkeys, grouse, New World quail, Old World quail, partridges, ptarmigans, junglefowl, peafowl, ducks, geese, swans, emus, and ostriches.

As used herein, “improved” should be taken broadly to encompass improvement of a characteristic of interest, as compared to a control group, or as compared to a known average quantity associated with the characteristic in question. For example, “improved” feed efficiency associated with application of a beneficial microbe, or bioensembles, of the disclosure can be demonstrated by comparing the feed efficiency of poultry treated by the microbes taught herein to the feed efficiency of poultry not treated. In the present disclosure, “improved” does not necessarily demand that the data be statistically significant (i.e. p<0.05); rather, any quantifiable difference demonstrating that one value (e.g. the average treatment value) is different from another (e.g. the average control value) can rise to the level of “improved.”

As used herein, “inhibiting and suppressing” and like terms should not be construed to require complete inhibition or suppression, although this may be desired in some embodiments.

The term “marker” or “unique marker” as used herein is an indicator of unique microorganism type, microorganism strain or activity of a microorganism strain. A marker can be measured in biological samples and includes without limitation, a nucleic acid-based marker such as a ribosomal RNA gene, a peptide- or protein-based marker, and/or a metabolite or other small molecule marker.

The term “metabolite” as used herein is an intermediate or product of metabolism. A metabolite in one embodiment is a small molecule. Metabolites have various functions, including in fuel, structural, signaling, stimulatory and inhibitory effects on enzymes, as a cofactor to an enzyme, in defense, and in interactions with other organisms (such as pigments, odorants and pheromones). A primary metabolite is directly involved in normal growth, development and reproduction. A secondary metabolite is not directly involved in these processes but usually has an important ecological function. Examples of metabolites include but are not limited to antibiotics and pigments such as resins and terpenes, etc. Some antibiotics use primary metabolites as precursors, such as actinomycin which is created from the primary metabolite, tryptophan. Metabolites, as used herein, include small, hydrophilic carbohydrates; large, hydrophobic lipids and complex natural compounds.

As used herein, the term “genotype” refers to the genetic makeup of an individual cell, cell culture, tissue, organism, or group of organisms.

As used herein, the term “allele(s)” means any of one or more alternative forms of a gene, all of which alleles relate to at least one trait or characteristic. In a diploid cell, the two alleles of a given gene occupy corresponding loci on a pair of homologous chromosomes. Since the present disclosure, in embodiments, relates to QTLs, i.e. genomic regions that may comprise one or more genes or regulatory sequences, it is in some instances more accurate to refer to “haplotype” (i.e. an allele of a chromosomal segment) instead of “allele”, however, in those instances, the term “allele” should be understood to comprise the term “haplotype”. Alleles are considered identical when they express a similar phenotype. Differences in sequence are possible but not important as long as they do not influence phenotype.

As used herein, the term “locus” (loci plural) means a specific place or places or a site on a chromosome where for example a gene or genetic marker is found.

As used herein, the term “genetically linked” refers to two or more traits that are co-inherited at a high rate during breeding such that they are difficult to separate through crossing.

A “recombination” or “recombination event” as used herein refers to a chromosomal crossing over or independent assortment. The term “recombinant” refers to an organism having a new genetic makeup arising as a result of a recombination event.

As used herein, the term “molecular marker” or “genetic marker” refers to an indicator that is used in methods for visualizing differences in characteristics of nucleic acid sequences. Examples of such indicators are restriction fragment length polymorphism (RFLP) markers, amplified fragment length polymorphism (AFLP) markers, single nucleotide polymorphisms (SNPs), insertion mutations, microsatellite markers (SSRs), sequence-characterized amplified regions (SCARs), cleaved amplified polymorphic sequence (CAPS) markers or isozyme markers or combinations of the markers described herein which defines a specific genetic and chromosomal location. Markers further include polynucleotide sequences encoding 16S or 18S rRNA, and internal transcribed spacer (ITS) sequences, which are sequences found between small-subunit and large-subunit rRNA genes that have proven to be especially useful in elucidating relationships or distinctions among when compared against one another. Mapping of molecular markers in the vicinity of an allele is a procedure which can be performed by the average person skilled in molecular-biological techniques.

The primary structure of major rRNA subunit 16S comprise a particular combination of conserved, variable, and hypervariable regions that evolve at different rates and enable the resolution of both very ancient lineages such as domains, and more modern lineages such as genera. The secondary structure of the 16S subunit include approximately 50 helices which result in base pairing of about 67% of the residues. These highly conserved secondary structural features are of great functional importance and can be used to ensure positional homology in multiple sequence alignments and phylogenetic analysis. Over the previous few decades, the 16S rRNA gene has become the most sequenced taxonomic marker and is the cornerstone for the current systematic classification of bacteria and archaea (Yarza et al. 2014. Nature Rev. Micro. 12:635-45).

A sequence identity of 94.5% or lower for two 16S rRNA genes is strong evidence for distinct genera, 86.5% or lower is strong evidence for distinct families, 82% or lower is strong evidence for distinct orders, 78.5% is strong evidence for distinct classes, and 75% or lower is strong evidence for distinct phyla. The comparative analysis of 16S rRNA gene sequences enables the establishment of taxonomic thresholds that are useful not only for the classification of cultured microorganisms but also for the classification of the many environmental sequences. Yarza et al. 2014. Nature Rev. Micro. 12:635-45).

As used herein, the term “trait” refers to a characteristic or phenotype. For example, in the context of some embodiments of the present disclosure; quantity of eggs produced, efficiency of feed utilization, amount of feces produced, susceptibility to gut pathogens, and a decrease in mortality rates, among others. Desirable traits may also include other characteristics, including but not limited to: an increase in weight; an increase in egg production; an increase of musculature; an increase of vitamins in eggs; an increase of fatty acid concentration in the gastrointestinal tract; and increase in egg volume; an improved efficiency in feed utilization and digestibility; an increase in polysaccharide and lignin degradation; an increase in fat, starch, and protein digestion; an increase in vitamin availability; an increase in mineral availability; an increase in amino acid availability; improved gastrointestinal development; increasing villi length and surface area; pH balance in the gastrointestinal tract; pH increase in the gastrointestinal tract, pH decrease in the gastrointestinal tract, a reduction in methane and/or nitrous oxide emissions; a reduction in manure production; an improved efficiency of nitrogen utilization; an improved efficiency of phosphorous utilization; an increased resistance to colonization of pathogenic microbes that colonize chickens; an improvement in meat properties, reduced mortality, increased production of antimicrobials, increased clearance of pathogenic microbes, increased resistance to colonization of pathogenic microbes that infect chickens, increased resistance to colonization of pathogenic microbes that infect humans improved gut health, etc.; wherein said increase, decrease, or reduction is determined by comparing against an animal not having been administered a composition of the present disclosure.

A trait may be inherited in a dominant or recessive manner, or in a partial or incomplete-dominant manner. A trait may be monogenic (i.e. determined by a single locus) or polygenic (i.e. determined by more than one locus) or may also result from the interaction of one or more genes with the environment.

In the context of this disclosure, traits may also result from the interaction of one or more avian genes and one or more microorganism genes.

As used herein, the term “homozygous” means a genetic condition existing when two identical alleles reside at a specific locus, but are positioned individually on corresponding pairs of homologous chromosomes in the cell of a diploid organism. Conversely, as used herein, the term “heterozygous” means a genetic condition existing when two different alleles reside at a specific locus, but are positioned individually on corresponding pairs of homologous chromosomes in the cell of a diploid organism.

As used herein, the term “phenotype” refers to the observable characteristics of an individual cell, cell culture, organism (e.g., bird), or group of organisms which results from the interaction between that individual's genetic makeup (i.e., genotype) and the environment.

As used herein, the term “chimeric” or “recombinant” when describing a nucleic acid sequence or a protein sequence refers to a nucleic acid, or a protein sequence, that links at least two heterologous polynucleotides, or two heterologous polypeptides, into a single macromolecule, or that re-arranges one or more elements of at least one natural nucleic acid or protein sequence. For example, the term “recombinant” can refer to an artificial combination of two otherwise separated segments of sequence, e.g., by chemical synthesis or by the manipulation of isolated segments of nucleic acids by genetic engineering techniques.

As used herein, a “synthetic nucleotide sequence” or “synthetic polynucleotide sequence” is a nucleotide sequence that is not known to occur in nature or that is not naturally occurring. Generally, such a synthetic nucleotide sequence will comprise at least one nucleotide difference when compared to any other naturally occurring nucleotide sequence.

As used herein, the term “nucleic acid” refers to a polymeric form of nucleotides of any length, either ribonucleotides or deoxyribonucleotides, or analogs thereof. This term refers to the primary structure of the molecule, and thus includes double- and single-stranded DNA, as well as double- and single-stranded RNA. It also includes modified nucleic acids such as methylated and/or capped nucleic acids, nucleic acids containing modified bases, backbone modifications, and the like. The terms “nucleic acid” and “nucleotide sequence” are used interchangeably.

As used herein, the term “gene” refers to any segment of DNA associated with a biological function. Thus, genes include, but are not limited to, coding sequences and/or the regulatory sequences required for their expression. Genes can also include non-expressed DNA segments that, for example, form recognition sequences for other proteins. Genes can be obtained from a variety of sources, including cloning from a source of interest or synthesizing from known or predicted sequence information, and may include sequences designed to have desired parameters.

As used herein, the term “homologous” or “homologue” or “ortholog” is known in the art and refers to related sequences that share a common ancestor or family member and are determined based on the degree of sequence identity. The terms “homology,” “homologous,” “substantially similar” and “corresponding substantially” are used interchangeably herein. They refer to nucleic acid fragments wherein changes in one or more nucleotide bases do not affect the ability of the nucleic acid fragment to mediate gene expression or produce a certain phenotype. These terms also refer to modifications of the nucleic acid fragments of the instant disclosure such as deletion or insertion of one or more nucleotides that do not substantially alter the functional properties of the resulting nucleic acid fragment relative to the initial, unmodified fragment. It is therefore understood, as those skilled in the art will appreciate, that the disclosure encompasses more than the specific exemplary sequences. These terms describe the relationship between a gene found in one species, subspecies, variety, cultivar or strain and the corresponding or equivalent gene in another species, subspecies, variety, cultivar or strain. For purposes of this disclosure homologous sequences are compared. “Homologous sequences” or “homologues” or “orthologs” are thought, believed, or known to be functionally related. A functional relationship may be indicated in any one of a number of ways, including, but not limited to: (a) degree of sequence identity and/or (b) the same or similar biological function. Preferably, both (a) and (b) are indicated. Homology can be determined using software programs readily available in the art, such as those discussed in Current Protocols in Molecular Biology (F. M. Ausubel et al., eds., 1987) Supplement 30, section 7.718, Table 7.71. Some alignment programs are MacVector (Oxford Molecular Ltd, Oxford, U.K.), ALIGN Plus (Scientific and Educational Software, Pennsylvania) and AlignX (Vector NTI, Invitrogen, Carlsbad, Calif.). Another alignment program is Sequencher (Gene Codes, Ann Arbor, Mich.), using default parameters.

As used herein, the term “nucleotide change” refers to, e.g., nucleotide substitution, deletion, and/or insertion, as is well understood in the art. For example, mutations contain alterations that produce silent substitutions, additions, or deletions, but do not alter the properties or activities of the encoded protein or how the proteins are made.

As used herein, the term “protein modification” refers to, e.g., amino acid substitution, amino acid modification, deletion, and/or insertion, as is well understood in the art.

As used herein, the term “at least a portion” or “fragment” of a nucleic acid or polypeptide means a portion having the minimal size characteristics of such sequences, or any larger fragment of the full length molecule, up to and including the full length molecule. A fragment of a polynucleotide of the disclosure may encode a biologically active portion of a genetic regulatory element. A biologically active portion of a genetic regulatory element can be prepared by isolating a portion of one of the polynucleotides of the disclosure that comprises the genetic regulatory element and assessing activity as described herein. Similarly, a portion of a polypeptide may be 4 amino acids, 5 amino acids, 6 amino acids, 7 amino acids, and so on, going up to the full length polypeptide. The length of the portion to be used will depend on the particular application. A portion of a nucleic acid useful as a hybridization probe may be as short as 12 nucleotides; in some embodiments, it is 20 nucleotides. A portion of a polypeptide useful as an epitope may be as short as 4 amino acids. A portion of a polypeptide that performs the function of the full-length polypeptide would generally be longer than 4 amino acids.

Variant polynucleotides also encompass sequences derived from a mutagenic and recombinogenic procedure such as DNA shuffling. Strategies for such DNA shuffling are known in the art. See, for example, Stemmer (1994) PNAS 91:10747-10751; Stemmer (1994) Nature 370:389-391; Crameri et al. (1997) Nature Biotech. 15:436-438; Moore et al. (1997) J. Mol. Biol. 272:336-347; Zhang et al. (1997) PNAS 94:4504-4509; Crameri et al. (1998) Nature 391:288-291; and U.S. Pat. Nos. 5,605,793 and 5,837,458. For PCR amplifications of the polynucleotides disclosed herein, oligonucleotide primers can be designed for use in PCR reactions to amplify corresponding DNA sequences from cDNA or genomic DNA extracted from any organism of interest. Methods for designing PCR primers and PCR cloning are generally known in the art and are disclosed in Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual (2nd ed., Cold Spring Harbor Laboratory Press, Plainview, N.Y.). See also Innis et al., eds. (1990) PCR Protocols: A Guide to Methods and Applications (Academic Press, New York); Innis and Gelfand, eds. (1995) PCR Strategies (Academic Press, New York); and Innis and Gelfand, eds. (1999) PCR Methods Manual (Academic Press, New York). Known methods of PCR include, but are not limited to, methods using paired primers, nested primers, single specific primers, degenerate primers, gene-specific primers, vector-specific primers, partially-mismatched primers, and the like.

The term “primer” as used herein refers to an oligonucleotide which is capable of annealing to the amplification target allowing a DNA polymerase to attach, thereby serving as a point of initiation of DNA synthesis when placed under conditions in which synthesis of primer extension product is induced, i.e., in the presence of nucleotides and an agent for polymerization such as DNA polymerase and at a suitable temperature and pH. The (amplification) primer is preferably single stranded for maximum efficiency in amplification. Preferably, the primer is an oligodeoxyribonucleotide. The primer must be sufficiently long to prime the synthesis of extension products in the presence of the agent for polymerization. The exact lengths of the primers will depend on many factors, including temperature and composition (A/T vs. G/C content) of primer. A pair of bi-directional primers consists of one forward and one reverse primer as commonly used in the art of DNA amplification such as in PCR amplification.

The terms “stringency” or “stringent hybridization conditions” refer to hybridization conditions that affect the stability of hybrids, e.g., temperature, salt concentration, pH, formamide concentration and the like. These conditions are empirically optimized to maximize specific binding and minimize non-specific binding of primer or probe to its target nucleic acid sequence. The terms as used include reference to conditions under which a probe or primer will hybridize to its target sequence, to a detectably greater degree than other sequences (e.g. at least 2-fold over background). Stringent conditions are sequence dependent and will be different in different circumstances. Longer sequences hybridize specifically at higher temperatures. Generally, stringent conditions are selected to be about 5° C. lower than the thermal melting point (Tm) for the specific sequence at a defined ionic strength and pH. The Tm is the temperature (under defined ionic strength and pH) at which 50% of a complementary target sequence hybridizes to a perfectly matched probe or primer. Typically, stringent conditions will be those in which the salt concentration is less than about 1.0 M Na+ ion, typically about 0.01 to 1.0 M Na+ ion concentration (or other salts) at pH 7.0 to 8.3 and the temperature is at least about 30° C. for short probes or primers (e.g. 10 to 50 nucleotides) and at least about 60° C. for long probes or primers (e.g. greater than 50 nucleotides). Stringent conditions may also be achieved with the addition of destabilizing agents such as formamide. Exemplary low stringent conditions or “conditions of reduced stringency” include hybridization with a buffer solution of 30% formamide, 1 M NaCl, 1% SDS at 37° C. and a wash in 2×SSC at 40° C. Exemplary high stringency conditions include hybridization in 50% formamide, 1M NaCl, 1% SDS at 37° C., and a wash in 0.1×SSC at 60° C. Hybridization procedures are well known in the art and are described by e.g. Ausubel et al., 1998 and Sambrook et al., 2001. In some embodiments, stringent conditions are hybridization in 0.25 M Na2HPO4 buffer (pH 7.2) containing 1 mM Na2EDTA, 0.5-20% sodium dodecyl sulfate at 45° C., such as 0.5%, 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19% or 20%, followed by a wash in 5×SSC, containing 0.1% (w/v) sodium dodecyl sulfate, at 55° C. to 65° C.

As used herein, “promoter” refers to a DNA sequence capable of controlling the expression of a coding sequence or functional RNA. The promoter sequence consists of proximal and more distal upstream elements, the latter elements often referred to as enhancers. Accordingly, an “enhancer” is a DNA sequence that can stimulate promoter activity, and may be an innate element of the promoter or a heterologous element inserted to enhance the level or tissue specificity of a promoter. Promoters may be derived in their entirety from a native gene, or be composed of different elements derived from different promoters found in nature, or even comprise synthetic DNA segments. It is understood by those skilled in the art that different promoters may direct the expression of a gene in different tissues or cell types, or at different stages of development, or in response to different environmental conditions. It is further recognized that since in most cases the exact boundaries of regulatory sequences have not been completely defined, DNA fragments of some variation may have identical promoter activity.

As used herein, a “constitutive promoter” is a promoter which is active under most conditions and/or during most development stages. There are several advantages to using constitutive promoters in expression vectors used in biotechnology, such as: high level of production of proteins used to select transgenic cells or organisms; high level of expression of reporter proteins or scorable markers, allowing easy detection and quantification; high level of production of a transcription factor that is part of a regulatory transcription system; production of compounds that requires ubiquitous activity in the organism; and production of compounds that are required during all stages of development. Non-limiting exemplary constitutive promoters include, CaMV 35S promoter, opine promoters, ubiquitin promoter, alcohol dehydrogenase promoter, etc.

As used herein, a “non-constitutive promoter” is a promoter which is active under certain conditions, in certain types of cells, and/or during certain development stages. For example, tissue specific, tissue preferred, cell type specific, cell type preferred, inducible promoters, and promoters under development control are non-constitutive promoters. Examples of promoters under developmental control include promoters that preferentially initiate transcription in certain tissues.

As used herein, “inducible” or “repressible” promoter is a promoter which is under chemical or environmental factors control. Examples of environmental conditions that may affect transcription by inducible promoters include anaerobic conditions, certain chemicals, the presence of light, acidic or basic conditions, etc.

As used herein, a “tissue specific” promoter is a promoter that initiates transcription only in certain tissues. Unlike constitutive expression of genes, tissue-specific expression is the result of several interacting levels of gene regulation. As such, in the art sometimes it is preferable to use promoters from homologous or closely related species to achieve efficient and reliable expression of transgenes in particular tissues. This is one of the main reasons for the large amount of tissue-specific promoters isolated from particular tissues found in both scientific and patent literature.

As used herein, the term “operably linked” refers to the association of nucleic acid sequences on a single nucleic acid fragment so that the function of one is regulated by the other. For example, a promoter is operably linked with a coding sequence when it is capable of regulating the expression of that coding sequence (i.e., that the coding sequence is under the transcriptional control of the promoter). Coding sequences can be operably linked to regulatory sequences in a sense or antisense orientation. In another example, the complementary RNA regions of the disclosure can be operably linked, either directly or indirectly, 5′ to the target mRNA, or 3′ to the target mRNA, or within the target mRNA, or a first complementary region is 5′ and its complement is 3′ to the target mRNA.

As used herein, the phrases “recombinant construct”, “expression construct”, “chimeric construct”, “construct”, and “recombinant DNA construct” are used interchangeably herein. A recombinant construct comprises an artificial combination of nucleic acid fragments, e.g., regulatory and coding sequences that are not found together in nature. For example, a chimeric construct may comprise regulatory sequences and coding sequences that are derived from different sources, or regulatory sequences and coding sequences derived from the same source, but arranged in a manner different than that found in nature. Such construct may be used by itself or may be used in conjunction with a vector. If a vector is used then the choice of vector is dependent upon the method that will be used to transform host cells as is well known to those skilled in the art. For example, a plasmid vector can be used. The skilled artisan is well aware of the genetic elements that must be present on the vector in order to successfully transform, select and propagate host cells comprising any of the isolated nucleic acid fragments of the disclosure. The skilled artisan will also recognize that different independent transformation events will result in different levels and patterns of expression (Jones et al., (1985) EMBO J. 4:2411-2418; De Almeida et al., (1989) Mol. Gen. Genetics 218:78-86), and thus that multiple events must be screened in order to obtain lines displaying the desired expression level and pattern. Such screening may be accomplished by Southern analysis of DNA, Northern analysis of mRNA expression, immunoblotting analysis of protein expression, or phenotypic analysis, among others. Vectors can be plasmids, viruses, bacteriophages, pro-viruses, phagemids, transposons, artificial chromosomes, and the like, that replicate autonomously or can integrate into a chromosome of a host cell. A vector can also be a naked RNA polynucleotide, a naked DNA polynucleotide, a polynucleotide composed of both DNA and RNA within the same strand, a poly-lysine-conjugated DNA or RNA, a peptide-conjugated DNA or RNA, a liposome-conjugated DNA, or the like, that is not autonomously replicating. As used herein, the term “expression” refers to the production of a functional end-product e.g., an mRNA or a protein (precursor or mature).

In some embodiments, the cell or organism has at least one heterologous trait. As used herein, the term “heterologous trait” refers to a phenotype imparted to a transformed host cell or transgenic organism by an exogenous DNA segment, heterologous polynucleotide or heterologous nucleic acid. Various changes in phenotype are of interest to the present disclosure, including but not limited to increasing a fowl's yield of an economically important trait (e.g., eggs, egg volume, poultry weight, etc.) and the like. These results can be achieved by providing expression of heterologous products or increased expression of endogenous products in organisms using the methods and compositions of the present disclosure. In some embodiments, the isolated microbial strains of the present disclosure further encompass mutants thereof. In some embodiments, the present disclosure further contemplates microbial strains having all of the identifying characteristics of the presently disclosed microbial strains.

As used herein, the term “MIC” means maximal information coefficient. MIC is a type of nonparamentric analysis that identifies a score (MIC score) between active microbial strains of the present disclosure and at least one measured metadata (e.g., increase in weight). Further, U.S. application Ser. No. 15/217,575, filed on Jul. 22, 2016 (issued as U.S. Pat. No. 9,540,676 on Jan. 10, 2017) is hereby incorporated by reference in its entirety.

The maximal information coefficient (MIC) is then calculated between strains and metadata and between strains as seen in FIG. 2, 2009 . Results are pooled to create a list of all relationships and their corresponding MIC scores. If the relationship scores below a given threshold, the relationship is deemed/identified as irrelevant. If the relationship is above a given threshold, the relationship deemed/identified as relevant, and is further subject to network analysis. The following code fragment shows an exemplary methodology for such analysis, according to one embodiment:

Read total list of relationships file as links threshold = 0.8 for i in range(len(links)):  if links >= threshold   mulitiplier[i] = 1  else   mulitiplier[i] = 0 end if link_temp = multiplier*links final_links = links_temp[links_temp != 0] savetxt(output_file,final_links) output_file.close( )

In some embodiments, the compositions of the present disclosure comprise one or more bacteria and/or one or more fungus that have a MIC score of at least about 0.1, 0.15, 0.2, 0.25, 0.3, 0.35, 0.4, 0.45, 0.5, 0.55, 0.6, 0.7, 0.75, 0.8, 0.85, 0.9, or 0.95.

With regard to MIC scores a cut-off based on this score may be used to define useful and non-useful microorganisms with respect to the improvement of specific traits. The point at which data points on a curve transition from a log scale to a linear scale (with regard to the slope) is the inflection point. Organisms with MIC scores that fall below the inflection point are generally non-useful, while the organisms with MIC scores that are found above the inflection point are generally useful, as it pertains to the specific characteristic being evaluated for the MIC score.

Based on the output of the network analysis, active strains are selected for preparing products (e.g., ensembles, aggregates, and/or other synthetic groupings) containing the selected strains. The output of the network analysis can also be used to inform the selection of strains for further product composition testing, as seen in FIG. 2, 2010 .

The use of thresholds is discussed above for analyses and determinations. Thresholds can be, depending on the implementation and application: (1) empirically determined (e.g., based on distribution levels, setting a cutoff at a number that removes a specified or significant portion of low level reads); (2) any non-zero value; (3) percentage/percentile based; (4) only strains whose normalized second marker (i.e., activity) reads is greater than normalized first marker (cell count) reads; (5) log 2 fold change between activity and quantity or cell count; (6) normalized second marker (activity) reads is greater than mean second marker (activity) reads for entire sample (and/or sample set); and/or any magnitude threshold described above in addition to a statistical threshold (i.e., significance testing). The following example provides thresholding detail for distributions of RNA-based second marker measurements with respect to DNA-based first marker measurements, according to one embodiment.

As used herein “shelf-stable” refers to a functional attribute and new utility acquired by the microbes formulated according to the disclosure, which enable said microbes to exist in a useful/active state outside of their natural environment in the gastrointestinal tract (i.e. a markedly different characteristic). Thus, shelf-stable is a functional attribute created by the formulations/compositions of the disclosure and denoting that the microbe formulated into a shelf-stable composition can exist outside the gastrointestinal tract and under ambient conditions for a period of time that can be determined depending upon the particular formulation utilized, but in general means that the microbes can be formulated to exist in a composition that is stable under ambient conditions for at least a few days and generally at least one week. Accordingly, a “shelf-stable poultry supplement” is a composition comprising one or more microbes of the disclosure, said microbes formulated in a composition, such that the composition is stable under ambient conditions for at least one week, meaning that the microbes comprised in the composition (e.g. whole cell, spore, or lysed cell) are able to impart one or more beneficial phenotypic properties to poultry when administered (e.g. increased weight gain, increased eggshell density, improved gastrointestinal health, and/or modulation of the gastrointestinal microbiome)

In aspects, the aforementioned microbial species—that is, a purified microbial population that comprises a bacteria with a 16S nucleic acid sequence, and/or a fungi with an ITS nucleic acid sequence, which is at least about 97% identical to a nucleic acid sequence selected from the group consisting of: SEQ ID NOs: 1-387—are members of a Markush group, as the present disclosure illustrates that the members belong to a class of microbes characterized by various physical and functional attributes, which can include any of the following: a) the ability to convert a carbon source into a volatile fatty acid such as acetate, butyrate, propionate, or combinations thereof; b) the ability to degrade a soluble or insoluble carbon source; c) the ability to impart an increase in weight gain to poultry administered the microbe(s); d) the ability to modulate the microbiome of the gastrointestinal tract of poultry administered the microbe; e) the ability to be formulated into a shelf-stable composition; f) the ability to exhibit a decrease in feed conversion ratio in poultry having been administered the microbe(s); g) the ability to impart a decrease in pathogen-associated lesion formation in the gastrointestinal tract; h) the ability to impart a decrease in pathogenic microbes in the gastrointestinal tract; and/or i) possessing a MIC score of at least about 0.2 if a bacteria and possessing a MIC score of at least about 0.2 if a fungi. Thus, the members of the Markush group possess at least one property in common, which can be responsible for their function in the claimed relationship.

In some embodiments, the isolated microbial strains of the present disclosure further encompass mutants thereof. In some embodiments, the present disclosure further contemplates microbial strains having all of the identifying characteristics of the presently disclosed microbial strains.

Isolated Microbes

In some aspects, the present disclosure provides isolated microbes, including novel strains of microbes, presented in Table 1 and Table 3.

In other aspects, the present disclosure provides isolated whole microbial cultures of the microbes identified in Table 1 and Table 3. These cultures may comprise microbes at various concentrations.

In some aspects, the disclosure provides for utilizing one or more microbes selected from Table 1 and Table 3 to increase a phenotypic trait of interest in poultry.

In some embodiments, the disclosure provides isolated microbial species belonging to taxonomic families of Lactobacillaceae, Lachnospiraceae, Ruminococcaceae, Peptostreptococcaceae, Streptosporangiaceae, Leuconostocaceae, Microbacteriaceae, Micromonosporaceae, Clostridiaceae, Pseudomonadaceae, Streptococcaceae, Bacillaceae, Bacteroidaceae, Nectriaceae, Corynebacteriaceae, Rhodobacteraceae, and Hypocreaceae.

In further embodiments, isolated microbial species may be selected from genera of family Lactobacillaceae, including Lactobacillus, Pediococcus, Paralactobacillus, and Sharpea.

In further embodiments, isolated microbial species may be selected from genera of family Lachnospiraceae, including Butyrivibrio, Roseburia, Lachnospira, Acetitomaculum, Coprococcus, Johnsonella, Catonella, Pseudobutyrivibrio, Syntrophococcus, Sporobacterium, Parasporobacterium, Lachnobacterium, Shuttleworthia, Dorea, Anaerostipes, Hespellia, Marvinbryantia, Oribacterium, Moryella, Blautia, Robinsoniella, Cellulosilyticum, Lachnoanaerobaculum, Stomatobaculum, Fusicatenibacter, Acetatifactor, and Eisenbergiella.

In further embodiments, isolated microbial species may be selected from genera of family Ruminococcaceae, including Ruminococcus, Acetivibrio, Sporobacter, Anaerofilium, Papillibacter, Oscillospira, Gemmiger, Faecalibacterium, Fastidiosipila, Anaerotruncus, Ethanolingenens, Acetanaerobacterium, Subdoligranulum, Hydrogenoanaerobacterium, and Candidadus Soleaferrea.

In further embodiments, isolated microbial species may be selected from genera of family Peptostreptococcaceae, including Anaerosphaera, Filifactor, Peptostreptococcus, Sporacetigenium, and Tepidibacter.

In further embodiments, isolated microbial species may be selected from genera of family Streptosporangiaceae, including Acrocarpospora, Herbidospora, Microbispora, Microtetraspora, Nonomuraea, Planobispora, Planomonospora, Planotetraspora, Sphaerisporangium, Streptosporangium, Thermoactinospora, Thermocatellispora, and Thermopolyspora.

In further embodiments, isolated microbial species may be selected from genera of family Leuconostocaceae, including Fructobacillus, Leuconostoc, Oenococcus, and Weissella.

In further embodiments, isolated microbial species may be selected from genera of family Microbacteriaceae, including Agreia, Agrococcus, Agromyces, Alpinomonas, Amnibacterium, Aureobacterium, Chryseoglobus, Clavibacter, Compostimonas, Cryobacterium, Curtobacterium, Diaminobutyricimonas, Frigoribacterium, Frondihabitans, Glacibacter, Gryllotalpicola, Gulosibacter, Herbiconiux, Homoserinimonas, Humibacter, Klugiella, Labedella, Leifsonia, Leucobacter, Lysinimonas, Marisediminicola, Microbacterium, Microcella, Microterricola, Mycetocola, Okibacterium, Phycicola, Plantibacter, Pontimonas, Pseudoclavibacter, Rathayibacter, Rhodoglobus, Salinibacterium, Schumanella, Subtercola, Yonghaparkia, and Zimmermannella.

In further embodiments, isolated microbial species may be selected from genera of family Micromonosporaceae, including Actinaurispora, Actinocatenispora, Actinoplanes, Allocatelliglobosispora, Amorphosporangium, Ampullariella, Asanoa, Catelliglobosispora, Catenuloplanes, Couchioplanes, Dactylosporangium, Hamadaea, Jishengella, Krasilnikovia, Longispora, Luedemannella, Micromonospora, Phytohabitans, Phytomonospora, Pilimelia, Planopolyspora, Planosporangium, Plantactinospora, Polymorphospora, Pseudosporangium, Rugosimonospora, Salinispora, Spirilliplanes, Verrucosispora, Virgisporangium, and Xiangella.

In further embodiments, isolated microbial species may be selected from genera of family Clostridiaceae, including Acetanaerobacterium, Acetivibrio, Acidaminobacter, Alkaliphilus, Anaerobacter, Anaerostipes, Anaerotruncus, Anoxynatronum, Bryantella, Butyricicoccus, Caldanaerocella, Caloramator, Caloranaerobacter, Caminicella, Candidatus Arthromitus, Clostridium, Coprobacillus, Ethanologenbacterium, Faecalibacterium, Garciella, Guggenheimella, Hespellia, Linmingia, Natronincola, Oxobacter, Parasporobacterium, Sarcina, Soehngenia, Sporobacter, Subdoligranulum, Tepidibacter, Tepidimicrobium, Thermobrachium, Thermohalobacter, and Tindallia.

In further embodiments, isolated microbial species may be selected from genera of family Pseudomonadaceae, including Acomonas, Azomonotrichon, Azorhizophilus, Azotobacter, Chryseomonas, Flavimonas, Mesophilobacter, Permianibacter, Pseudomonas, Rhizobacter, Rugamonas, Serpens, and Thiopseudomonas.

In further embodiments, isolated microbial species may be selected from genera of family Nectriaceae, including Albonectria, Allonectella, Calonectria, Calostilbe, Calostilbella, Campylocarpon, Corallomycetella, Cosmospora, Cylindrocarpon, Cylindrocladiella, Cylindrocladium, Fusarium, Fusicolla, Gibberella, Glionectria, Haematonectria, Lanatonectria, Leuconectria, Nectria, Necticladiella, Neocosmoprora, Neonectria, Ophionectria, Pleogibberella, Pseudonectria, Rubrinectria, Stalagmites, Tubercularia, Viridispora, Xenocalonectria, Xenonectriella, and Zythiostroma.

In some embodiments, the disclosure provides isolated microbial species belonging to genera of. Hypocreaceae, including Aphysiostroma, Cladobotryum, Gliocladium, Hypocrea, Hypocreopsis, Hypomyces, Mycogone, Nectria, Podostroma, Protocrea, Rogersonia, Sarawakus, Sepedonium, Sphaerostilbella, Sporophagomyces, Stephanoma, and Trichoderma.

In some embodiments, one or more microbes from the taxa disclosed herein are utilized to impart one or more beneficial properties or improved traits to poultry production.

Furthermore, the disclosure relates to microbes having characteristics substantially similar to that of a microbe identified in Table 1 and/or Table 3.

The isolated microbial species, and novel strains of said species, identified in the present disclosure, are able to impart beneficial properties or traits to poultry production.

For instance, the isolated microbes described in Table 1 and Table 3, or bioensembles of said microbes, are able to increase feed efficiency. The increase can be quantitatively measured, for example, by measuring the effect that said microbial application has upon the modulation of feed efficiency. In some embodiments, feed efficiency is represented by the feed conversion ratio, which is calculated by measuring desirable animal output produced per pound of feed consumed. With regard to poultry, the desirable output is typically pounds of meat produced per pound of feed consumed.

In some embodiments, the isolated microbial strains are microbes of the present disclosure that have been genetically modified. In some embodiments, the genetically modified or recombinant microbes comprise polynucleotide sequences which do not naturally occur in said microbes. In some embodiments, the microbes may comprise heterologous polynucleotides. In further embodiments, the heterologous polynucleotides may be operably linked to one or more polynucleotides native to the microbes. In some embodiments, the isolated microbial strains of the present disclosure further encompass mutants thereof. In some embodiments, the present disclosure further contemplates microbial strains having all of the identifying characteristics of the presently disclosed microbial strains.

In some embodiments, the heterologous polynucleotides may be reporter genes or selectable markers. In some embodiments, reporter genes may be selected from any of the family of fluorescence proteins (e.g., GFP, RFP, YFP, and the like), β-galactosidase, luciferase. In some embodiments, selectable markers may be selected from neomycin phosphotransferase, hygromycin phosphotransferase, aminoglycoside adenyltransferase, dihydrofolate reductase, acetolactase synthase, bromoxynil nitrilase, O-glucuronidase, dihydrogolate reductase, and chloramphenicol acetyltransferase. In some embodiments, the heterologous polynucleotide may be operably linked to one or more promoter.

In some embodiments the isolated microbial strains express transgenic or native enzymes selected from cellulases (endocellulases, exocellulases, glucosidases), pectinases, amylases, amylopectinases, ligninases, and phytases

In some embodiments, the species of the taxa provided in Table 4 are not known to have been utilized in compositions for administration to animals.

TABLE 4 Taxa (largely Genera) of the present disclosure not known to have been utilized in animal agriculture. Corynebacterium Verrucosispora Clostridium XIVa Clostridium Clostridium XI Blautia Faecalibacterium Pseudomonas Hydrogenoanaerobacterium Sporobacter Acrocarpospora Clostridium III Subdoligranulum Paracoccus Leuconostoc Cellulosilyticum Lachnospiracea Ruminococcus Anaerofilum Roseburia Microbacterium Clostridium XIVb Verrucosispora Bacteroides

In some aspects, the disclosure provides microbial bioensembles comprising a combination of at least any two microbes selected from amongst the microbes identified in Table 1 and Table 3.

In certain embodiments, the bioensembles of the present disclosure comprise two microbes, or three microbes, or four microbes, or five microbes, or six microbes, or seven microbes, or eight microbes, or nine microbes, or ten or more microbes. Said microbes of the bioensembles are different microbial species, or different strains of a microbial species.

In some embodiments, the disclosure provides bioensembles, comprising: at least one or at least two isolated microbial species belonging to genera of: Lactobacillus, Clostridium, Faecalibacter, Hydrogenoanaerobacterium, Acrocarpospora, Bacillus, Subdoligranulum, Leuconostoc, Lachnospiracea, Anaerofilum, Microbacterium, Verrucosispora, Anaerofilum, Blautia, Pseudomonas, Sporobacter, Corynebacterium, Streptococcus, Paracoccus, Cellulosilyticum, Ruminococcus, Rosebura, Bacteroides, Filobasidium, Gibberella, Alatospora, Pichia, and Candida. Particular novel strains of species of these aforementioned genera can be found in Table 1 and Table 3.

In some embodiments, the disclosure provides bioensembles, comprising: at least one or at least two isolated microbial species belonging to the family of: Lactobacillaceae, Lachnospiraceae, Ruminococcaceae, Peptostreptococcaceae, Streptosporangiaceae, Leuconostocaceae, Microbacteriaceae, Micromonosporaceae, Clostridiaceae, Pseudomonadales, Nectriaceae, and Hypocreaceae; wherein Lachnospiraceae can be further specific to Clostridium clusters XIVa and XIVb; and wherein Peptostreptococcaceae can be further specific to Clostridium cluster XI. Particular novel strains of species of these aforementioned genera can be found in Table 1 and Table 3.

In particular aspects, the disclosure provides microbial bioensembles, comprising species as grouped in Tables 5-11. With respect to Tables 5-11, the letters A through I represent a non-limiting selection of microbes of the present disclosure, defined as:

-   -   A=Strain designation Ascusbbr_578 identified in Table 1;     -   B=Strain designation Ascusbbr_1436 identified in Table 1;     -   C=Strain designation Ascusbbr_33B identified in Table 1;     -   D=Strain designation Ascusbbr_409 identified in Table 1;     -   E=Strain designation Ascusbbr_185064 identified in Table 1;     -   F=Strain designation Ascusbbr_5796 identified in Table 1;     -   G=Strain designation Ascusbbr_105932 identified in Table 1;     -   H=Strain designation Ascusbbr_4729 identified in Table 1; and     -   I=Strain designation Ascusbbr_2676 identified in Table 1.

TABLE 5 Eight and Nine Strain Bioensembles A, B, C, D, E, F, G, H A, B, C, D, E, F, G, I A, B, C, D, E, F, H, I A, B, C, D, E, G, H, I A, B, C, D, F, G, H, I A, B, C, E, F, G, H, I A, B, D, E, F, G, H, I A, C, D, E, F, G, H, I B, C, D, E, F, G, H, I A, B, C, D, E, F, G, H, I

TABLE 6 Seven Strain Bioensembles A, B, C, D, E, F, G A, B, C, D, E, F, H A, B, C, D, E, F, I A, B, C, D, E, G, H A, B, C, D, E, G, I A, B, C, D, E, H, I A, B, C, D, F, G, H A, B, C, D, F, G, I A, B, C, D, F, H, I A, B, C, D, G, H, I A, B, C, E, F, G, H A, B, C, E, F, G, I A, B, C, E, F, H, I A, B, C, E, G, H, I A, B, C, F, G, H, I A, B, D, E, F, G, H A, B, D, E, F, G, I A, B, D, E, F, H, I A, B, D, E, G, H, I A, B, D, F, G, H, I A, B, E, F, G, H, I A, C, D, E, F, G, H A, C, D, E, F, G, I A, C, D, E, F, H, I A, C, D, E, G, H, I A, C, D, F, G, H, I A, C, E, F, G, H, I A, D, E, F, G, H, I B, C, D, E, F, G, H B, C, D, E, F, G, I B, C, D, E, F, H, I B, C, D, E, G, H, I B, C, D, F, G, H, I B, C, E, F, G, H, I B, D, E, F, G, H, I C, D, E, F, G, H, I

TABLE 7 Six Strain Bioensembles A, B, C, D, E, F A, B, C, D, E, G A, B, C, D, E, H A, B, C, D, E, I A, B, C, D, F, G A, B, C, D, F, H A, B, C, D, F, I A, B, C, D, G, H A, B, C, D, G, I A, B, C, D, H, I A, B, C, E, F, G A, B, C, E, F, H A, B, C, E, F, I A, B, C, E,G, H A, B, C, E, G, I A, B, C, E, H, I A, B, C, F, G, H A, B, C, F, G, I A, B, C, F, H, I A, B, C, G, H, I A, B, D, E, F, G A, B, D, E, F, H A, B, D, E, F, I A, B, D, E, G, H A, B, D, E, G, I A, B, D, E, H, I A, B, D, F, G, H A, B, D, F, G, I D, E, F, G, H, I C, E, F, G, H, I A, B, D, F, H, I A, B, D, G, H, I A, B, E, F, G, H A, B, E, F, G, I A, B, E, F, H, I A, B, E, G, H, I A, B, F, G, H, I A, C, D, E, F, G A, C, D, E, F, H A, C, D, E, F, I A, C, D, E, G, H A, C, D, E, G, I A, C, D, E, H, I A, C, D, F, G, H A, C, D, F, G, I A, C, D, F, H, I A, C, D, G, H, I A, C, E, F, G, H A, C, E, F, G, I A, C, E, F, H, I A, C, E,G, H, I A, C, F, G, H, I A, D, E, F, G, H A, D, E, F, G, I A, D, E, F, H, I A, D, E, G, H, I A, D, F, G, H, I A, E, F, G, H, I B, C, D, E, F, G B, C, D, E, F, H B, C, D, E, F, I B, C, D, E, G, H B, C, D, E, G, I B, C, D, E, H, I B, C, D, F, G, H B, C, D, F, G, I B, C, D, F, H, I B, C, D, G, H, I B, C, E, F, G, H B, C, E, F, G, I B, C, E, F, H, I B, C, E, G, H, I B, C, F, G, H, I B, D, E, F, G, H B, D, E, F, G, I B, D, E, F, H, I B, D, E,G, H, I B, D, F, G, H, I B, E, F, G, H, I C, D, E, F, G, H C, D, E, F, G, I C, D, E, F, H, I C, D, E, G, H, I C, D, F, G, H, I

TABLE 8 Five Strain Bioensembles A, B, C, D, E A, B, C, D, F A, B, C, D, G A, B, C, D, H A, B, C, D, I A, B, C, E, F A, B, C, E, G A, B, C, E, H A, B, C, F, H A, B, C, F, G A, B, C, F, I A, B, C, G, H A, B, C, G, I A, B, C, H, I A, B, D, E, F A, B, D, E, G A, B, D, E, I A, B, D, F, G A, B, D, F, H A, B, D, FJ A, B, D, G, H A, B, D, G, I A, B, D, H, I A, B, E, F, G A, B, E, F, I A, B, E, G, H A, B, E, G, I A, B, E, H, I A, B, F, G, H A, B, F, G, I A, B, F, H, I A, B, G, H, I A, C, D, E, G A, C, D, E, H A, C, D, E, I A, C, D, F, G A, C, D, F, H A, C, D, F, I A, C, D, G, H A, C, D, G, I A, C, E, F, G A, C, E, F, H A, C, E, F, I A, C, E, G, H A, C, E, G, I A, C, E, H, I A, C, F, G, H A, C, F, G, I A, C, G, H, I A, D, E, F, G A, D, E, F, H A, D, E, F, I A, D, E, G, H A, D, E, G, I A, D, E, H, I A, D, F, G, H A, D, F, H, I A, D, G, H, I A, E, F, G, H A, E, F, G, I A, E, F, H, I A, E, G, H, I A, F, G, H, I B, C, D, E, F B, C, D, E, H B, C, D, E, I B, C, D, F, G B, C, D, F, H B, C, D, F, I B, C, D, G, H B, C, D, G, I B, C, D, H, I B, C, E, F, H B, C, E, F, I B, C, E, G, H B, C, E, G, I B, C, E, H, I B, C, F, G, H B, C, F, G, I B, C, F, H, I B, D, E, F, G B, D, E, F, H B, D, E, F, I B, D, E, G, H B, D, E, G, I B, D, E, H, I B, D, F, G, H B, D, F, G, I B, D, G, H, I B, E, F, G, H B, E, F, G, I B, E, F, H, I B, E, G, H, I B, F, G, H, I C, D, E, F, G C, D, E, F, H C, D, E, G, H C, D, E, G, I C, D, E, H, I C, D, F, G, H C, D, F, G, I C, D, F, H, I C, D, G, H, I C, E, F, G, H C, E, F, H, I C, E, G, H, I C, F, G, H, I D, E, F, G, H D, E, F, G, I D, E, F, H, I D, E, G, H, I D, F, G, H, I A, B, C, E, I A, B, D, E, H A, B, E, F, H A, C, D, E, F A, C, D, H, I A, C, F, H, I A, D, F, G, I B, C, D, E, G B, C, E, F, G B, C, G, H, I B, D, F, H, I C, D, E, F, I C, E, F, G, I E, F, G, H, I

TABLE 9 Four Strain Bioensembles A, B, C, D A, B, C, E A, B, C, F A, B, C, G A, B, C, H A, B, C, I A, B, D, E A, B, D, F D, G, H, I A, B, D, G A, B, D, H A, B, D, I A, B, E, F A, B, E, G A, B, E, H A, B, E, I A, B, F, G E, F, G, H A, B, F, H A, D, F, H A, D, F, I A, D, G, H A, D, G, I A, D, H, I A, E, F, G A, E, F, H E, F, G, I A, B, F, I A, B, G, H A, B, G, I A, B, H, I A, C, D, E A, C, D, F A, C, D, G A, C, D, H E, F, H, I A, C, D, I A, C, E, F A, C, E, G A, C, E, H A, C, E, I A, C, F, G A, C, F, H A, C, F, I E, G, H, I A, C, G, H A, C, G, I A, C, H, I A, D, E, F A, D, E, G A, D, E, H A, D, E, I A, D, F, G F, G, H, I A, E, F, I A, E, G, H A, E, G, I A, E, H, I A, F, G, H A, F, G, I A, F, H, I A, G, H, I D, E, F, H B, C, D, E B, C, D, F B, C, D, G B, C, D, H B, C, D, I B, C, E, F B, C, E, G B, C, E, H D, E, F, I B, C, E, I B, C, F, G B, C, F, H B, C, F, I B, C, G, H B, C, G, I B, C, H, I B, D, E, F D, E, G, H B, D, E, G B, D, E, H B, D, E, I B, D, F, G B, D, F, H B, D, F, I B, D, G, H B, D, G, I D, E, G, I B, D, H, I B, E, F, G B, E, F, H B, E, F, I B, E, G, H B, E, G, I B, E, H, I B, F, G, H D, E, H, I B, F, G, I B, F, H, I B, G, H, I C, D, E, F C, D, E, G C, D, E, H C, D, E, I C, D, F, G D, F, G, H C, D, F, H C, D, F, I C, D, G, H C, D, G, I C, D, H, I C, E, F, G C, E, F, H C, E, F, I D, F, G, I C, E, G, H C, E, G, I C, E, H, I C, F, G, H C, F, G, I C, F, H, I C, G, H, I D, E, F, G D, F, H, I

TABLE 10 Three Strain Bioensembles A, B, C A, B, D A, B, E A, B, F A, B, G A, B, H A, B, I A, C, D A, C, E G, H, I E, F, H A, C, F A, C, G A, C, H A, C, I A, D, E A, D, F A, D, G A, D, H A, D, I F, H, I E, F, G A, E, F A, E, G A, E, H A, E, I A, F, G A, F, H A, F, I A, G, H A, G, I F, G, I D, H, I A, H, I B, C, D B, C, E B, C, F B, C, G B, C, H B, C, I B, D, E B, D, F F, G, H D, G, I B, D, G B, D, H B, D, I B, E, F B, E, G B, E, H B, E, I B, F, G B, F, H E, H, I E, F, I B, F, I B, G, H B, G, I B, H, I C, D, E C, D, F C, D, G C, D, H C, D, I E, G, I D, G, H C, E, F C, E, G C, E, H C, E, I C, F, G C, F, H C, F, I C, G, H C, G, I E, G, H D, F, I C, H, I D, E, F D, E, G D, E, H D, E, I D, F, G D, F, H

TABLE 11 Two Strain Bioensembles A, B A, C A, D A, E A, F A, G A, H A, I B, C B, D B, E B, F B, G B, H B, I C, D C, E C, F C, G C, H C, I D, E D, F D, G D, H D, I E, F E, G E, H E, I F, G F, H F, I G, H G, I H, I

In some embodiments, the microbial bioensembles may be selected from any member group from Tables 5-11.

Isolated Microbes—Source Material

The microbes of the present disclosure were obtained, among other places, at various locales in the United States from the gastrointestinal tract of poultry.

Isolated Microbes—Microbial Culture Techniques

The microbes of Table 1 and Table 3 were matched to their nearest taxonomic groups by utilizing classification tools of the Ribosomal Database Project (RDP) for 16s rRNA sequences and the User-friendly Nordic ITS Ectomycorrhiza (UNITE) database for ITS rRNA sequences. Examples of matching microbes to their nearest taxa may be found in Lan et al. (2012. PLOS one. 7(3):e32491), Schloss and Westcott (2011. Appl. Environ. Microbiol. 77(10):3219-3226), and Koljalg et al. (2005. New Phytologist. 166(3):1063-1068).

The isolation, identification, and culturing of the microbes of the present disclosure can be effected using standard microbiological techniques. Examples of such techniques may be found in Gerhardt, P. (ed.) Methods for General and Molecular Microbiology. American Society for Microbiology, Washington, D.C. (1994) and Lennette, E. H. (ed.) Manual of Clinical Microbiology, Third Edition. American Society for Microbiology, Washington, D.C. (1980), each of which is incorporated by reference.

Isolation can be effected by streaking the specimen on a solid medium (e.g., nutrient agar plates) to obtain a single colony, which is characterized by the phenotypic traits described hereinabove (e.g., Gram positive/negative, capable of forming spores aerobically/anaerobically, cellular morphology, carbon source metabolism, acid/base production, enzyme secretion, metabolic secretions, etc.) and to reduce the likelihood of working with a culture which has become contaminated.

For example, for microbes of the disclosure, biologically pure isolates can be obtained through repeated subculture of biological samples, each subculture followed by streaking onto solid media to obtain individual colonies or colony forming units. Methods of preparing, thawing, and growing lyophilized bacteria are commonly known, for example, Gherna, R. L. and C. A. Reddy. 2007. Culture Preservation, p 1019-1033. In C. A. Reddy, T. J. Beveridge, J. A. Breznak, G. A. Marzluf, T. M. Schmidt, and L. R. Snyder, eds. American Society for Microbiology, Washington, D.C., 1033 pages; herein incorporated by reference. Thus freeze dried liquid formulations and cultures stored long term at −70° C. in solutions containing glycerol are contemplated for use in providing formulations of the present disclosure.

The microbes of the disclosure can be propagated in a liquid medium under aerobic conditions, or alternatively anaerobic conditions. Medium for growing the bacterial strains of the present disclosure includes a carbon source, a nitrogen source, and inorganic salts, as well as specially required substances such as vitamins, amino acids, nucleic acids and the like. Examples of suitable carbon sources which can be used for growing the microbes include, but are not limited to, starch, peptone, yeast extract, amino acids, sugars such as glucose, arabinose, mannose, glucosamine, maltose, and the like; salts of organic acids such as acetic acid, fumaric acid, adipic acid, propionic acid, citric acid, gluconic acid, malic acid, pyruvic acid, malonic acid and the like; alcohols such as ethanol and glycerol and the like; oil or fat such as soybean oil, rice bran oil, olive oil, corn oil, sesame oil. The amount of the carbon source added varies according to the kind of carbon source and is typically between 1 to 100 gram(s) per liter of medium. Preferably, glucose, starch, and/or peptone is contained in the medium as a major carbon source, at a concentration of 0.1-5% (W/V). Examples of suitable nitrogen sources which can be used for growing the bacterial strains of the present disclosure include, but are not limited to, amino acids, yeast extract, tryptone, beef extract, peptone, potassium nitrate, ammonium nitrate, ammonium chloride, ammonium sulfate, ammonium phosphate, ammonia or combinations thereof. The amount of nitrogen source varies according to the type of nitrogen source, typically between 0.1 to 30 grams per liter of media. The inorganic salts, potassium dihydrogen phosphate, dipotassium hydrogen phosphate, disodium hydrogen phosphate, magnesium sulfate, magnesium chloride, ferric sulfate, ferrous sulfate, ferric chloride, ferrous chloride, manganous sulfate, manganous chloride, zinc sulfate, zinc chloride, cupric sulfate, calcium chloride, sodium chloride, calcium carbonate, sodium carbonate can be used alone or in combination. The amount of inorganic acid varies according to the kind of the inorganic salt, typically between 0.001 to 10 grams per liter of medium. Examples of specially required substances include, but are not limited to, vitamins, nucleic acids, yeast extract, peptone, meat extract, malt extract, dried yeast and combinations thereof. Cultivation can be effected at a temperature, which allows the growth of the microbial strains, essentially, between 20° C. and 46° C. In some aspects, a temperature range is 30° C.-39° C. For optimal growth, in some embodiments, the medium can be adjusted to pH 6.0-7.4. It will be appreciated that commercially available media may also be used to culture the microbial strains, such as Nutrient Broth or Nutrient Agar available from Difco, Detroit, Mich. It will be appreciated that cultivation time may differ depending on the type of culture medium used and the concentration of sugar as a major carbon source.

In some aspects, cultivation lasts between 24-96 hours. Microbial cells thus obtained are isolated using methods, which are well known in the art. Examples include, but are not limited to, membrane filtration and centrifugal separation. The pH may be adjusted using sodium hydroxide and the like and the culture may be dried using a freeze dryer, until the water content becomes equal to 4% or less. Microbial co-cultures may be obtained by propagating each strain as described hereinabove. In some aspects, microbial multi-strain cultures may be obtained by propagating two or more of the strains described hereinabove. It will be appreciated that the microbial strains may be cultured together when compatible culture conditions can be employed.

Isolated Microbes—Microbial Strains

Microbes can be distinguished into a genus based on polyphasic taxonomy, which incorporates all available phenotypic and genotypic data into a consensus classification (Vandamme et al. 1996. Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol Rev 1996, 60:407-438). One accepted genotypic method for defining species is based on overall genomic relatedness, such that strains which share approximately 70% or more relatedness using DNA-DNA hybridization, with 5° C. or less ΔT_(m) (the difference in the melting temperature between homologous and heterologous hybrids), under standard conditions, are considered to be members of the same species. Thus, populations that share greater than the aforementioned 70% threshold can be considered to be variants of the same species. Another accepted genotypic method for defining species is to isolate marker genes of the present disclosure, sequence these genes, and align these sequenced genes from multiple isolates or variants. The microbes are interpreted as belonging to the same species if one or more of the sequenced genes share at least 97% sequence identity.

The 16S or 18S rRNA sequences or ITS sequences are often used for making distinctions between species and strains, in that if one of the aforementioned sequences shares less than a specified % sequence identity from a reference sequence, then the two organisms from which the sequences were obtained are said to be of different species or strains.

Thus, one could consider microbes to be of the same species, if they share at least 94.5%, 95%, 97%, 98%, or 99% sequence identity across the 16S or 18S rRNA sequence, or the ITS1 or ITS2 sequence.

Further, one could define microbial strains of a species, as those that share at least 94.5%, 95%, 97%, 98%, or 99% sequence identity across the 16S or 18S rRNA sequence, or the ITS1 or ITS2 sequence.

Sequence identifiers of the present disclosure consist of SEQ ID NOs:1-387. SEQ ID NOs:1-50 and 59-387 are bacterial polynucleotide sequences encoding 16S rRNA. SEQ ID NOs:51-58 are fungal polynucleotide sequences encoding ITS sequences.

In one embodiment, microbial strains of the present disclosure include those that comprise polynucleotide sequences that share at least 70%, 75%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity with any one of SEQ ID NOs:1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 39, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 380, 381, 382, 383, 384, 385, 386, and 387. In a further embodiment, microbial strains of the present disclosure include those that comprise polynucleotide sequences that share at least 70%, 75%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity with any one of SEQ ID NOs:1-387.

Comparisons may also be made with 23S rRNA sequences against reference sequences.

Unculturable microbes often cannot be assigned to a definite species in the absence of a phenotype determination, the microbes can be given a Candidatus designation within a genus provided their 16S or 18S rRNA sequences or ITS sequences subscribes to the principles of identity with known species.

One approach is to observe the distribution of a large number of strains of closely related species in sequence space and to identify clusters of strains that are well resolved from other clusters. This approach has been developed by using the concatenated sequences of multiple core (house-keeping) genes to assess clustering patterns, and has been called multilocus sequence analysis (MLSA) or multilocus sequence phylogenetic analysis. MLSA has been used successfully to explore clustering patterns among large numbers of strains assigned to very closely related species by current taxonomic methods, to look at the relationships between small numbers of strains within a genus, or within a broader taxonomic grouping, and to address specific taxonomic questions. More generally, the method can be used to ask whether bacterial species exist—that is, to observe whether large populations of similar strains invariably fall into well-resolved clusters, or whether in some cases there is a genetic continuum in which clear separation into clusters is not observed.

In order to more accurately make a determination of genera, a determination of phenotypic traits, such as morphological, biochemical, and physiological characteristics are made for comparison with a reference genus archetype. The colony morphology can include color, shape, pigmentation, production of slime, etc. Features of the cell are described as to shape, size, Gram reaction, extracellular material, presence of endospores, flagella presence and location, motility, and inclusion bodies. Biochemical and physiological features describe growth of the organism at different ranges of temperature, pH, salinity and atmospheric conditions, growth in presence of different sole carbon and nitrogen sources. One of ordinary skill in the art would be reasonably apprised as to the phenotypic traits that define the genera of the present disclosure.

In one embodiment, the microbes taught herein were identified utilizing 16S rRNA gene sequences and ITS sequences. It is known in the art that 16S rRNA contains hypervariable regions that can provide species/strain-specific signature sequences useful for bacterial identification, and that ITS sequences can also provide species/strain-specific signature sequences useful for fungal identification.

Phylogenetic analysis using the rRNA genes and/or ITS sequences are used to define “substantially similar” species belonging to common genera and also to define “substantially similar” strains of a given taxonomic species. Furthermore, physiological and/or biochemical properties of the isolates can be utilized to highlight both minor and significant differences between strains that could lead to advantageous behavior in poultry.

Compositions of the present disclosure may include combinations of fungal spores and bacterial spores, fungal spores and bacterial vegetative cells, fungal vegetative cells and bacterial spores, fungal vegetative cells and bacterial vegetative cells, fungal vegetative cells and fungal spores, and bacterial vegetative cells and bacterial spores. In some embodiments, compositions of the present disclosure comprise bacteria only in the form of spores. In some embodiments, compositions of the present disclosure comprise bacteria only in the form of vegetative cells. In some embodiments, compositions of the present disclosure comprise fungi only in the form of spores. In some embodiments, compositions of the present disclosure comprise fungi only in the form of vegetative cells. In some embodiments, compositions of the present disclosure comprise bacteria in the absence of fungi. In some embodiments, compositions of the present disclosure comprise fungi in the absence of bacteria. In some embodiments, compositions of the present disclosure comprise VBNC bacteria and/or fungi. In some embodiments, compositions of the present disclosure include dormant bacteria and/or fungi.

Bacterial spores may include endospores and akinetes. Fungal spores may include statismospores, ballistospores, autospores, aplanospores, zoospores, mitospores, megaspores, microspores, meiospores, chlamydospores, urediniospores, teliospores, oospores, carpospores, tetraspores, sporangiospores, zygospores, basidiospores, ascospores, and asciospores.

In some embodiments, spores of the composition germinate upon administration to animals of the present disclosure. In some embodiments, spores of the composition germinate only upon administration to animals of the present disclosure.

Microbial Compositions

In some embodiments, the microbes of the disclosure are combined into microbial compositions.

In some embodiments, the microbial compositions include poultry feed, such as cereals (barley, maize, oats, and the like); starches (tapioca and the like); oilseed cakes; and vegetable wastes. In some embodiments, the microbial compositions include vitamins, minerals, trace elements, emulsifiers, aromatizing products, binders, colorants, odorants, thickening agents, and the like. In some embodiments, the microbial compositions include one or more of an ionophore; vaccine; antibiotic; antihelmintic; virucide; nematicide; amino acids such as methionine, glycine, and arginine; fish oil; oregano; prebiotics; and biologically active molecules such as enzymes.

In some embodiments, the microbial compositions of the present disclosure are solid. Where solid compositions are used, it may be desired to include one or more carrier materials including, but not limited to: mineral earths such as silicas, talc, kaolin, limestone, chalk, clay, dolomite, diatomaceous earth; calcium sulfate; magnesium sulfate; magnesium oxide; zeolites, calcium carbonate; magnesium carbonate; trehalose; chitosan; shellac; albumins; starch; skim-milk powder; sweet-whey powder; maltodextrin; lactose; inulin; dextrose; products of vegetable origin such as cereal meals, tree bark meal, wood meal, and nutshell meal; products comprising typical poultry food stuffs such as ground corn, barley, oats, and the like.

In some embodiments, the microbial compositions of the present disclosure are liquid. In further embodiments, the liquid comprises a solvent that may include water or an alcohol or a saline or carbohydrate solution, and other animal-safe solvents. In some embodiments, the microbial compositions of the present disclosure include binders such as animal-safe polymers, carboxymethylcellulose, starch, polyvinyl alcohol, and the like.

In some embodiments, the microbial compositions of the present disclosure comprise thickening agents or gelling agents such as silica, clay, natural extracts of seeds or seaweed, synthetic derivatives of cellulose, guar gum, locust bean gum, alginates, and methylcelluloses. In some embodiments, the microbial compositions comprise anti-settling agents such as modified starches, polyvinyl alcohol, xanthan gum, and the like.

In some embodiments, the microbial compositions of the present disclosure comprise colorants including organic chromophores classified as nitroso; nitro; azo, including monoazo, bisazo and polyazo; acridine, anthraquinone, azine, diphenylmethane, indamine, indophenol, methine, oxazine, phthalocyanine, thiazine, thiazole, triarylmethane, xanthene. In some embodiments, the microbial compositions of the present disclosure comprise trace nutrients such as salts of iron, manganese, boron, copper, cobalt, molybdenum and zinc. In some embodiments, the microbial compositions comprise dyes, both natural and artificial. In some embodiments, the dye is green in color. In some embodiments, the dye is red in color.

In some embodiments, the microbial compositions of the present disclosure comprise an animal-safe virucide, bacteriocide, or nematicide.

In some embodiments, microbial compositions of the present disclosure comprise saccharides (e.g., monosaccharides, disaccharides, trisaccharides, polysaccharides, oligosaccharides, and the like), polymeric saccharides, lipids, polymeric lipids, lipopolysaccharides, proteins, polymeric proteins, lipoproteins, nucleic acids, nucleic acid polymers, silica, inorganic salts and combinations thereof. In a further embodiment, microbial compositions comprise polymers of agar, agarose, gelrite, and gellan gum, and the like. In some embodiments, microbial compositions comprise plastic capsules, emulsions (e.g., water and oil), membranes, and artificial membranes. In some embodiments, emulsions or linked polymer solutions may comprise microbial compositions of the present disclosure. See Harel and Bennett (U.S. Pat. No. 8,460,726B2). In one embodiment, the microbial composition comprises glucose. In one embodiment, formulations of the microbial composition comprise glucose.

In some embodiments, microbial compositions of the present disclosure comprise one or more oxygen scavengers, denitrifiers, nitrifiers, heavy metal chelators, and/or dechlorinators; and combinations thereof. In one embodiment, the one or more oxygen scavengers, denitrifiers, nitrifiers, heavy metal chelators, and/or dechlorinators are not chemically active once the microbial compositions are mixed with food and/or water to be administered to the poultry. In one embodiment, the one or more oxygen scavengers, denitrifiers, nitrifiers, heavy metal chelators, and/or dechlorinators are not chemically active when administered to the poultry.

In some embodiments, microbial compositions of the present disclosure occur in a solid form (e.g., dispersed lyophilized spores) or a liquid form (microbes interspersed in a storage medium). In some embodiments, microbial compositions of the present disclosure are added in dry form to a liquid to form a suspension immediately prior to administration.

In some embodiments, microbial compositions of the present disclosure comprise one or more preservatives. The preservatives may be in liquid or gas formulations. The preservatives may be selected from one or more of monosaccharide, disaccharide, trisaccharide, polysaccharide, acetic acid, ascorbic acid, calcium ascorbate, erythorbic acid, iso-ascorbic acid, erythrobic acid, potassium nitrate, sodium ascorbate, sodium erythorbate, sodium iso-ascorbate, sodium nitrate, sodium nitrite, nitrogen, benzoic acid, calcium sorbate, ethyl lauroyl arginate, methyl-p-hydroxy benzoate, methyl paraben, potassium acetate, potassium benzoate, potassium bisulphite, potassium diacetate, potassium lactate, potassium metabisulphite, potassium sorbate, propyl-p-hydroxy benzoate, propyl paraben, sodium acetate, sodium benzoate, sodium bisulphite, sodium nitrite, sodium diacetate, sodium lactate, sodium metabisulphite, sodium salt of methyl-p-hydroxy benzoic acid, sodium salt of propyl-p-hydroxy benzoic acid, sodium sulphate, sodium sulfite, sodium dithionite, sulphurous acid, calcium propionate, dimethyl dicarbonate, natamycin, potassium sorbate, potassium bisulfite, potassium metabisulfite, propionic acid, sodium diacetate, sodium propionate, sodium sorbate, sorbic acid, ascorbic acid, ascorbyl palmitate, ascorbyl stearate, butylated hydro-xyanisole, butylated hydroxytoluene (BHT), butylated hydroxyl anisole (BHA), citric acid, citric acid esters of mono- and/or diglycerides, L-cysteine, L-cysteine hydrochloride, gum guaiacum, gum guaiac, lecithin, lecithin citrate, monoglyceride citrate, monoisopropyl citrate, propyl gallate, sodium metabisulphite, tartaric acid, tertiary butyl hydroquinone, stannous chloride, thiodipropionic acid, dilauryl thiodipropionate, distearyl thiodipropionate, ethoxyquin, sulfur dioxide, formic acid, or tocopherol(s).

In some embodiments, microbial compositions of the present disclosure include bacterial and/or fungal cells in spore form, vegetative cell form, dormant cell form, and/or lysed form. In one embodiment, the lysed cell form acts as a mycotoxin binder, e.g. mycotoxins binding to dead cells.

In some embodiments, the microbial compositions are shelf stable in a refrigerator (35-40° F.) for a period of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, or 60 days. In some embodiments, the microbial compositions are shelf stable in a refrigerator (35-40° F.) for a period of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, or 60 weeks.

In some embodiments, the microbial compositions are shelf stable at room temperature (68-72° F.) or between 50-77° F. for a period of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, or 60 days. In some embodiments, the microbial compositions are shelf stable at room temperature (68-72° F.) or between 50-77° F. for a period of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, or 60 weeks.

In some embodiments, the microbial compositions are shelf stable at −23-35° F. for a period of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, or 60 days. In some embodiments, the microbial compositions are shelf stable at −23-35° F. for a period of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, or 60 weeks.

In some embodiments, the microbial compositions are shelf stable at 77-100° F. for a period of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, or 60 days. In some embodiments, the microbial compositions are shelf stable at 77-100° F. for a period of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, or 60 weeks.

In some embodiments, the microbial compositions are shelf stable at 101-213° F. for a period of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, or 60 days. In some embodiments, the microbial compositions are shelf stable at 101-213° F. for a period of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, or 60 weeks.

In some embodiments, the microbial compositions of the present disclosure are shelf stable at refrigeration temperatures (35-40° F.), at room temperature (68-72° F.), between 50-77° F., between −23-35° F., between 70-100° F., or between 101-213° F. for a period of about 1 to 100, about 1 to 95, about 1 to 90, about 1 to 85, about 1 to 80, about 1 to 75, about 1 to 70, about 1 to 65, about 1 to 60, about 1 to 55, about 1 to 50, about 1 to 45, about 1 to 40, about 1 to 35, about 1 to 30, about 1 to 25, about 1 to 20, about 1 to 15, about 1 to 10, about 1 to 5, about 5 to 100, about 5 to 95, about 5 to 90, about 5 to 85, about 5 to 80, about 5 to 75, about 5 to 70, about 5 to 65, about 5 to 60, about 5 to 55, about 5 to 50, about 5 to 45, about 5 to 40, about 5 to 35, about 5 to 30, about 5 to 25, about 5 to 20, about 5 to 15, about 5 to 10, about 10 to 100, about 10 to 95, about 10 to 90, about 10 to 85, about 10 to 80, about 10 to 75, about 10 to 70, about 10 to 65, about 10 to 60, about 10 to 55, about 10 to 50, about 10 to 45, about 10 to 40, about 10 to 35, about 10 to 30, about 10 to 25, about 10 to 20, about 10 to 15, about 15 to 100, about 15 to 95, about 15 to 90, about 15 to 85, about 15 to 80, about 15 to 75, about 15 to 70, about 15 to 65, about 15 to 60, about 15 to 55, about 15 to 50, about 15 to 45, about 15 to 40, about 15 to 35, about 15 to 30, about 15 to 25, about 15 to 20, about 20 to 100, about 20 to 95, about 20 to 90, about 20 to 85, about 20 to 80, about 20 to 75, about 20 to 70, about 20 to 65, about 20 to 60, about 20 to 55, about 20 to 50, about 20 to 45, about 20 to 40, about 20 to 35, about 20 to 30, about 20 to 25, about 25 to 100, about 25 to 95, about 25 to 90, about 25 to 85, about 25 to 80, about 25 to 75, about 25 to 70, about 25 to 65, about 25 to 60, about 25 to 55, about 25 to 50, about 25 to 45, about 25 to 40, about 25 to 35, about 25 to 30, about 30 to 100, about 30 to 95, about 30 to 90, about 30 to 85, about 30 to 80, about 30 to 75, about 30 to 70, about 30 to 65, about 30 to 60, about 30 to 55, about 30 to 50, about 30 to 45, about 30 to 40, about 30 to 35, about 35 to 100, about 35 to 95, about 35 to 90, about 35 to 85, about 35 to 80, about 35 to 75, about 35 to 70, about 35 to 65, about 35 to 60, about 35 to 55, about 35 to 50, about 35 to 45, about 35 to 40, about 40 to 100, about 40 to 95, about 40 to 90, about 40 to 85, about 40 to 80, about 40 to 75, about 40 to 70, about 40 to 65, about 40 to 60, about 40 to 55, about 40 to 50, about 40 to 45, about 45 to 100, about 45 to 95, about 45 to 90, about 45 to 85, about 45 to 80, about 45 to 75, about 45 to 70, about 45 to 65, about 45 to 60, about 45 to 55, about 45 to 50, about 50 to 100, about 50 to 95, about 50 to 90, about 50 to 85, about 50 to 80, about 50 to 75, about 50 to 70, about 50 to 65, about 50 to 60, about 50 to 55, about 55 to 100, about 55 to 95, about 55 to 90, about 55 to 85, about 55 to 80, about 55 to 75, about 55 to 70, about 55 to 65, about 55 to 60, about 60 to 100, about 60 to 95, about 60 to 90, about 60 to 85, about 60 to 80, about 60 to 75, about 60 to 70, about 60 to 65, about 65 to 100, about 65 to 95, about 65 to 90, about 65 to 85, about 65 to 80, about 65 to 75, about 65 to 70, about 70 to 100, about 70 to 95, about 70 to 90, about 70 to 85, about 70 to 80, about 70 to 75, about 75 to 100, about 75 to 95, about 75 to 90, about 75 to 85, about 75 to 80, about 80 to 100, about 80 to 95, about 80 to 90, about 80 to 85, about 85 to 100, about 85 to 95, about 85 to 90, about 90 to 100, about 90 to 95, or 95 to 100 weeks

In some embodiments, the microbial compositions of the present disclosure are shelf stable at refrigeration temperatures (35-40° F.), at room temperature (68-72° F.), between 50-77° F., between −23-35° F., between 70-100° F., or between 101-213° F. for a period of 1 to 100, 1 to 95, 1 to 90, 1 to 85, 1 to 80, 1 to 75, 1 to 70, 1 to 65, 1 to 60, 1 to 55, 1 to 50, 1 to 45, 1 to 40, 1 to 35, 1 to 30, 1 to 25, 1 to 20, 1 to 15, 1 to 10, 1 to 5, 5 to 100, 5 to 95, 5 to 90, 5 to 85, 5 to 80, 5 to 75, 5 to 70, 5 to 65, 5 to 60, 5 to 55, 5 to 50, 5 to 45, 5 to 40, 5 to 35, 5 to 30, 5 to 25, 5 to 20, 5 to 15, 5 to 10, 10 to 100, 10 to 95, 10 to 90, 10 to 85, 10 to 80, 10 to 75, 10 to 70, 10 to 65, 10 to 60, 10 to 55, 10 to 50, 10 to 45, 10 to 40, 10 to 35, 10 to 30, 10 to 25, 10 to 20, 10 to 15, 15 to 100, 15 to 95, 15 to 90, 15 to 85, 15 to 80, 15 to 75, 15 to 70, 15 to 65, 15 to 60, 15 to 55, 15 to 50, 15 to 45, 15 to 40, 15 to 35, 15 to 30, 15 to 25, 15 to 20, 20 to 100, 20 to 95, 20 to 90, 20 to 85, 20 to 80, 20 to 75, 20 to 70, 20 to 65, 20 to 60, 20 to 55, 20 to 50, 20 to 45, 20 to 40, 20 to 35, 20 to 30, 20 to 25, 25 to 100, 25 to 95, 25 to 90, 25 to 85, 25 to 80, 25 to 75, 25 to 70, 25 to 65, 25 to 60, 25 to 55, 25 to 50, 25 to 45, 25 to 40, 25 to 35, 25 to 30, 30 to 100, 30 to 95, 30 to 90, 30 to 85, 30 to 80, 30 to 75, 30 to 70, 30 to 65, 30 to 60, 30 to 55, 30 to 50, 30 to 45, 30 to 40, 30 to 35, 35 to 100, 35 to 95, 35 to 90, 35 to 85, 35 to 80, 35 to 75, 35 to 70, 35 to 65, 35 to 60, 35 to 55, 35 to 50, 35 to 45, 35 to 40, 40 to 100, 40 to 95, 40 to 90, 40 to 85, 40 to 80, 40 to 75, 40 to 70, 40 to 65, 40 to 60, 40 to 55, 40 to 50, 40 to 45, 45 to 100, 45 to 95, 45 to 90, 45 to 85, 45 to 80, 45 to 75, 45 to 70, 45 to 65, 45 to 60, 45 to 55, 45 to 50, 50 to 100, 50 to 95, 50 to 90, 50 to 85, 50 to 80, 50 to 75, 50 to 70, 50 to 65, 50 to 60, 50 to 55, 55 to 100, 55 to 95, 55 to 90, 55 to 85, 55 to 80, 55 to 75, 55 to 70, 55 to 65, 55 to 60, 60 to 100, 60 to 95, 60 to 90, 60 to 85, 60 to 80, 60 to 75, 60 to 70, 60 to 65, 65 to 100, 65 to 95, 65 to 90, 65 to 85, 65 to 80, 65 to 75, 65 to 70, 70 to 100, 70 to 95, 70 to 90, 70 to 85, 70 to 80, 70 to 75, 75 to 100, 75 to 95, 75 to 90, 75 to 85, 75 to 80, 80 to 100, 80 to 95, 80 to 90, 80 to 85, 85 to 100, 85 to 95, 85 to 90, 90 to 100, 90 to 95, or 95 to 100 weeks.

In some embodiments, the microbial compositions of the present disclosure are shelf stable at refrigeration temperatures (35-40° F.), at room temperature (68-72° F.), between 50-77° F., between −23-35° F., between 70-100° F., or between 101-213° F. for a period of about 1 to 36, about 1 to 34, about 1 to 32, about 1 to 30, about 1 to 28, about 1 to 26, about 1 to 24, about 1 to 22, about 1 to 20, about 1 to 18, about 1 to 16, about 1 to 14, about 1 to 12, about 1 to 10, about 1 to 8, about 1 to 6, about 1 one 4, about 1 to 2, about 4 to 36, about 4 to 34, about 4 to 32, about 4 to 30, about 4 to 28, about 4 to 26, about 4 to 24, about 4 to 22, about 4 to 20, about 4 to 18, about 4 to 16, about 4 to 14, about 4 to 12, about 4 to 10, about 4 to 8, about 4 to 6, about 6 to 36, about 6 to 34, about 6 to 32, about 6 to 30, about 6 to 28, about 6 to 26, about 6 to 24, about 6 to 22, about 6 to 20, about 6 to 18, about 6 to 16, about 6 to 14, about 6 to 12, about 6 to 10, about 6 to 8, about 8 to 36, about 8 to 34, about 8 to 32, about 8 to 30, about 8 to 28, about 8 to 26, about 8 to 24, about 8 to 22, about 8 to 20, about 8 to 18, about 8 to 16, about 8 to 14, about 8 to 12, about 8 to 10, about 10 to 36, about 10 to 34, about 10 to 32, about 10 to 30, about 10 to 28, about 10 to 26, about 10 to 24, about 10 to 22, about 10 to 20, about 10 to 18, about 10 to 16, about 10 to 14, about 10 to 12, about 12 to 36, about 12 to 34, about 12 to 32, about 12 to 30, about 12 to 28, about 12 to 26, about 12 to 24, about 12 to 22, about 12 to 20, about 12 to 18, about 12 to 16, about 12 to 14, about 14 to 36, about 14 to 34, about 14 to 32, about 14 to 30, about 14 to 28, about 14 to 26, about 14 to 24, about 14 to 22, about 14 to 20, about 14 to 18, about 14 to 16, about 16 to 36, about 16 to 34, about 16 to 32, about 16 to 30, about 16 to 28, about 16 to 26, about 16 to 24, about 16 to 22, about 16 to 20, about 16 to 18, about 18 to 36, about 18 to 34, about 18 to 32, about 18 to 30, about 18 to 28, about 18 to 26, about 18 to 24, about 18 to 22, about 18 to 20, about 20 to 36, about 20 to 34, about 20 to 32, about 20 to 30, about 20 to 28, about 20 to 26, about 20 to 24, about 20 to 22, about 22 to 36, about 22 to 34, about 22 to 32, about 22 to 30, about 22 to 28, about 22 to 26, about 22 to 24, about 24 to 36, about 24 to 34, about 24 to 32, about 24 to 30, about 24 to 28, about 24 to 26, about 26 to 36, about 26 to 34, about 26 to 32, about 26 to 30, about 26 to 28, about 28 to 36, about 28 to 34, about 28 to 32, about 28 to 30, about 30 to 36, about 30 to 34, about 30 to 32, about 32 to 36, about 32 to 34, or about 34 to 36 months.

In some embodiments, the microbial compositions of the present disclosure are shelf stable at refrigeration temperatures (35-40° F.), at room temperature (68-72° F.), between 50-77° F., between −23-35° F., between 70-100° F., or between 101-213° F. for a period of 1 to 36 1 to 34 1 to 32 1 to 30 1 to 28 1 to 26 1 to 24 1 to 22 1 to 20 1 to 18 1 to 16 1 to 14 1 to 12 1 to 10 1 to 8 1 to 6 1 one 4 1 to 24 to 36 4 to 34 4 to 32 4 to 30 4 to 28 4 to 26 4 to 24 4 to 22 4 to 20 4 to 18 4 to 16 4 to 14 4 to 12 4 to 10 4 to 8 4 to 6 6 to 36 6 to 34 6 to 32 6 to 30 6 to 28 6 to 26 6 to 24 6 to 22 6 to 20 6 to 18 6 to 16 6 to 14 6 to 12 6 to 10 6 to 8 8 to 36 8 to 34 8 to 32 8 to 30 8 to 28 8 to 26 8 to 24 8 to 22 8 to 20 8 to 18 8 to 16 8 to 14 8 to 12 8 to 10 10 to 36 10 to 34 10 to 32 10 to 30 10 to 28 10 to 26 10 to 24 10 to 22 10 to 20 10 to 18 10 to 16 10 to 14 10 to 12 12 to 36 12 to 34 12 to 32 12 to 30 12 to 28 12 to 26 12 to 24 12 to 22 12 to 20 12 to 18 12 to 16 12 to 14 14 to 36 14 to 34 14 to 32 14 to 30 14 to 28 14 to 26 14 to 24 14 to 22 14 to 20 14 to 18 14 to 16 16 to 36 16 to 34 16 to 32 16 to 30 16 to 28 16 to 26 16 to 24 16 to 22 16 to 20 16 to 18 18 to 36 18 to 34 18 to 32 18 to 30 18 to 28 18 to 26 18 to 24 18 to 22 18 to 20 20 to 36 20 to 34 20 to 32 20 to 30 20 to 28 20 to 26 20 to 24 20 to 22 22 to 36 22 to 34 22 to 32 22 to 30 22 to 28 22 to 26 22 to 24 24 to 36 24 to 34 24 to 32 24 to 30 24 to 28 24 to 26 26 to 36 26 to 34 26 to 32 26 to 30 26 to 28 28 to 36 28 to 34 28 to 32 28 to 30 30 to 36 30 to 34 30 to 32 32 to 36 32 to 34, or about 34 to 36.

In some embodiments, the microbial compositions of the present disclosure are shelf stable at any of the disclosed temperatures and/or temperature ranges and spans of time at a relative humidity of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, or 98%.

Moisture content is a measurement of the total amount of water in a composition, usually expressed as a percentage of the total weight. The moisture content is a useful measurement for determining the dry weight of a composition, and it can be used to confirm whether the desiccation/drying process of a composition is complete. The moisture content is calculated by dividing the (wet weight of the composition minus the weight after desiccating/drying) by the wet weight of the composition, and multiplying by 100.

Moisture content defines the amount of water in a composition, but water activity explains how the water in the composition will react with microorganisms. The greater the water activity, the faster microorganisms are able to grow. Water activity is calculated by finding the ratio of the vapor pressure in a composition to the vapor pressure of pure water. More specifically, the water activity is the partial vapor pressure of water in a composition divided by the standard state partial vapor pressure of pure water. Pure distilled water has a water activity of 1. A determination of water activity of a composition is not the amount of water in a composition, rather it is the amount of excess amount of water that is available for microorganisms to use. Microorganisms have a minimal and optimal water activity for growth.

In some embodiments, the microbial compositions of the present disclosure are desiccated. A microbial composition is desiccated if the moisture content of the composition is between 0% and 20%.

In some embodiments, the microbial compositions of the present disclosure have a moisture content of about 0.5%, about 0.6%, about 0.7%, about 0.8%, about 0.9%, about 1%, about 2%, about 3%, about 4%, about 5%, about 6%, about 7%, about 8%, about 9%, about 10%, about 11%, about 12%, about 13%, about 14%, about 15%, about 16%, about 17%, about 18%, about 19%, about 20%, about 21%, about 22%, about 23%, about 24%, about 25%, about 26%, about 27%, about 28%, about 29%, about 30%, about 31%, about 32%, about 33%, about 34%, about 35%, about 36%, about 37%, about 38%, about 39%, about 40%, about 41%, about 42%, about 43%, about 44%, about 45%, about 46%, about 47%, about 48%, about 49%, about 50%, about 51%, about 52%, about 53%, about 54%, about 55%, about 56%, about 57%, about 58%, about 59%, about 60%, about 61%, about 62%, about 63%, about 64%, about 65%, about 66%, about 67%, about 68%, about 69%, about 70%, about 71%, about 72%, about 73%, about 74%, about 75%, about 76%, about 77%, about 78%, about 79%, about 80%, about 81%, about 82%, about 83%, about 84%, about 85%, about 86%, about 87%, about 88%, about 89%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or about 100%.

In some embodiments, the microbial compositions of the present disclosure have a moisture content of less than 0.5%, less than 0.6%, less than 0.7%, less than 0.8%, less than 0.9%, less than 1%, less than 2%, less than 3%, less than 4%, less than 5%, less than 6%, less than 7%, less than 8%, less than 9%, less than 10%, less than 11%, less than 12%, less than 13%, less than 14%, less than 15%, less than 16%, less than 17%, less than 18%, less than 19%, less than 20%, less than 21%, less than 22%, less than 23%, less than 24%, less than 25%, less than 26%, less than 27%, less than 28%, less than 29%, less than 30%, less than 31%, less than 32%, less than 33%, less than 34%, less than 35%, less than 36%, less than 37%, less than 38%, less than 39%, less than 40%, less than 41%, less than 42%, less than 43%, less than 44%, less than 45%, less than 46%, less than 47%, less than 48%, less than 49%, less than 50%, less than 51%, less than 52%, less than 53%, less than 54%, less than 55%, less than 56%, less than 57%, less than 58%, less than 59%, less than 60%, less than 61%, less than 62%, less than 63%, less than 64%, less than 65%, less than 66%, less than 67%, less than 68%, less than 69%, less than 70%, less than 71%, less than 72%, less than 73%, less than 74%, less than 75%, less than 76%, less than 77%, less than 78%, less than 79%, less than 80%, less than 81%, less than 82%, less than 83%, less than 84%, less than 85%, less than 86%, less than 87%, less than 88%, less than 89%, less than 90%, less than 91%, less than 92%, less than 93%, less than 94%, less than 95%, less than 96%, less than 97%, less than 98%, less than 99%, or less than 100%.

In some embodiments, the microbial compositions of the present disclosure have a moisture content of less than about 0.5%, less than about 0.6%, less than about 0.7%, less than about 0.8%, less than about 0.9%, less than about 1%, less than about 2%, less than about 3%, less than about 4%, less than about 5%, less than about 6%, less than about 7%, less than about 8%, less than about 9%, less than about 10%, less than about 11%, less than about 12%, less than about 13%, less than about 14%, less than about 15%, less than about 16%, less than about 17%, less than about 18%, less than about 19%, less than about 20%, less than about 21%, less than about 22%, less than about 23%, less than about 24%, less than about 25%, less than about 26%, less than about 27%, less than about 28%, less than about 29%, less than about 30%, less than about 31%, less than about 32%, less than about 33%, less than about 34%, less than about 35%, less than about 36%, less than about 37%, less than about 38%, less than about 39%, less than about 40%, less than about 41%, less than about 42%, less than about 43%, less than about 44%, less than about 45%, less than about 46%, less than about 47%, less than about 48%, less than about 49%, less than about 50%, less than about 51%, less than about 52%, less than about 53%, less than about 54%, less than about 55%, less than about 56%, less than about 57%, less than about 58%, less than about 59%, less than about 60%, less than about 61%, less than about 62%, less than about 63%, less than about 64%, less than about 65%, less than about 66%, less than about 67%, less than about 68%, less than about 69%, less than about 70%, less than about 71%, less than about 72%, less than about 73%, less than about 74%, less than about 75%, less than about 76%, less than about 77%, less than about 78%, less than about 79%, less than about 80%, less than about 81%, less than about 82%, less than about 83%, less than about 84%, less than about 85%, less than about 86%, less than about 87%, less than about 88%, less than about 89%, less than about 90%, less than about 91%, less than about 92%, less than about 93%, less than about 94%, less than about 95%, less than about 96%, less than about 97%, less than about 98%, less than about 99%, or less than about 100%.

In some embodiments, the microbial compositions of the present disclosure have a moisture content of 1% to 100%, 1% to 95%, 1% to 90%, 1% to 85%, 1% to 80%, 1% to 75%, 1% to 70%, 1% to 65%, 1% to 60%, 1% to 55%, 1% to 50%, 1% to 45%, 1% to 40%, 1% to 35%, 1% to 30%, 1% to 25%, 1% to 20%, 1% to 15%, 1% to 10%, 1% to 5%, 5% to 100%, 5% to 95%, 5% to 90%, 5% to 85%, 5% to 80%, 5% to 75%, 5% to 70%, 5% to 65%, 5% to 60%, 5% to 55%, 5% to 50%, 5% to 45%, 5% to 40%, 5% to 35%, 5% to 30%, 5% to 25%, 5% to 20%, 5% to 15%, 5% to 10%, 10% to 100%, 10% to 95%, 10% to 90%, 10% to 85%, 10% to 80%, 10% to 75%, 10% to 70%, 10% to 65%, 10% to 60%, 10% to 55%, 10% to 50%, 10% to 45%, 10% to 40%, 10% to 35%, 10% to 30%, 10% to 25%, 10% to 20%, 10% to 15%, 15% to 100%, 15% to 95%, 15% to 90%, 15% to 85%, 15% to 80%, 15% to 75%, 15% to 70%, 15% to 65%, 15% to 60%, 15% to 55%, 15% to 50%, 15% to 45%, 15% to 40%, 15% to 35%, 15% to 30%, 15% to 25%, 15% to 20%, 20% to 100%, 20% to 95%, 20% to 90%, 20% to 85%, 20% to 80%, 20% to 75%, 20% to 70%, 20% to 65%, 20% to 60%, 20% to 55%, 20% to 50%, 20% to 45%, 20% to 40%, 20% to 35%, 20% to 30%, 20% to 25%, 25% to 100%, 25% to 95%, 25% to 90%, 25% to 85%, 25% to 80%, 25% to 75%, 25% to 70%, 25% to 65%, 25% to 60%, 25% to 55%, 25% to 50%, 25% to 45%, 25% to 40%, 25% to 35%, 25% to 30%, 30% to 100%, 30% to 95%, 30% to 90%, 30% to 85%, 30% to 80%, 30% to 75%, 30% to 70%, 30% to 65%, 30% to 60%, 30% to 55%, 30% to 50%, 30% to 45%, 30% to 40%, 30% to 35%, 35% to 100%, 35% to 95%, 35% to 90%, 35% to 85%, 35% to 80%, 35% to 75%, 35% to 70%, 35% to 65%, 35% to 60%, 35% to 55%, 35% to 50%, 35% to 45%, 35% to 40%, 40% to 100%, 40% to 95%, 40% to 90%, 40% to 85%, 40% to 80%, 40% to 75%, 40% to 70%, 40% to 65%, 40% to 60%, 40% to 55%, 40% to 50%, 40% to 45%, 45% to 100%, 45% to 95%, 45% to 90%, 45% to 85%, 45% to 80%, 45% to 75%, 45% to 70%, 45% to 65%, 45% to 60%, 45% to 55%, 45% to 50%, 50% to 100%, 50% to 95%, 50% to 90%, 50% to 85%, 50% to 80%, 50% to 75%, 50% to 70%, 50% to 65%, 50% to 60%, 50% to 55%, 55% to 100%, 55% to 95%, 55% to 90%, 55% to 85%, 55% to 80%, 55% to 75%, 55% to 70%, 55% to 65%, 55% to 60%, 60% to 100%, 60% to 95%, 60% to 90%, 60% to 85%, 60% to 80%, 60% to 75%, 60% to 70%, 60% to 65%, 65% to 100%, 65% to 95%, 65% to 90%, 65% to 85%, 65% to 80%, 65% to 75%, 65% to 70%, 70% to 100%, 70% to 95%, 70% to 90%, 70% to 85%, 70% to 80%, 70% to 75%, 75% to 100%, 75% to 95%, 75% to 90%, 75% to 85%, 75% to 80%, 80% to 100%, 80% to 95%, 80% to 90%, 80% to 85%, 85% to 100%, 85% to 95%, 85% to 90%, 90% to 100%, 90% to 95%, or 95% to 100%.

Microbial compositions suitable for use in the present application are disclosed in Embree et al. (PCT/US2017/028015).

In some embodiments, the microbial compositions of the present disclosure possess a water activity of at least 0.05, at least 0.075, at least 0.1, at least 0.1.25, at least 0.15, at least 0.175, at least 0.2, at least 0.225, at least 0.25, at least 0.275, at least 0.3, at least 0.325, at least 0.35, at least 0.375, at least 0.4, at least 0.425, at least 0.45, at least 0.475, at least 0.5, at least 0.525, at least 0.55, at least 0.575, or at least 0.6.

In some embodiments, the microbial compositions of the present disclosure possess a water activity of less than 0.05, less than 0.075, less than 0.1, less than 0.1.25, less than 0.15, less than 0.175, less than 0.2, less than 0.225, less than 0.25, less than 0.275, less than 0.3, less than 0.325, less than 0.35, less than 0.375, less than 0.4, less than 0.425, less than 0.45, less than 0.475, less than 0.5, less than 0.525, less than 0.55, less than 0.575, or less than 0.6.

Poultry

Poultry include chickens (broilers/fryers/roasters/capons/roosters/stewing hens), turkeys, grouse, New World quail, Old World quail, partridges, ptarmigans, junglefowl, peafowl, ducks, geese, swans, emus, and ostriches.

Broiler chickens of the present disclosure include: Cobb 500, Cobb 700, Cobb Avian 48, Cobb Sasso, Ross 308, Ross 708, Ross PM3, Jersey Giant, Cornish Cross, Delaware, Dorking, Buckeye, Campine, Chantecler, Crevecoeur, Holland, Modern Game, Nankin, Redcap, Russian, Orloff, Spanish, Sultan, Sumatra, Yokohama, Andalusian, Buttercup, Cubalaya, Faverolles, Java, Lakenvelder, Langshan, Malay, Phoenix, Ancona, Aseel, Brahma, Catalana, Cochin, Cornish, Dominique, Hamburg, Houdan, La Fleche, Minorca, New Hampshire, Old English Game, Polish, Rhode Island White, Sebright, Shamo, Australorp, Leghorn, Orpington, Plymouth Rock, Rhode Island Red, Sussex, Wyandotte, Araucana, Iowa Blue, Lamona, Manx Rumpy, Naked Neck, Asil, Kadacknath Bursa, Hubbard, Hubbard, Cobb, Hubbard, Lohman, Anak 2000, Avian-34, Starbra, Sam Rat, Bowans, Hyline, BV-300, H & N Nick, Dekalb Lohman, ILI-80, Golden-92, Priya, Sonali, Devendra, B-77, Caribro-91, Varna, Caribro naked necked, Caribro multicolored, Aviagen, Ross, Arbor Acres, Indian River, Peterson, Cobb-Vantress, Avian Sasso, Hybro, Groupe Grimaud, Grimaud Frere, Ameraucana, Silkie, Marans, Rosecomb, Welsummer, Barnevelder, Bantam, Asil, Chantecler, Croad, Houdan, Pekin, Frizzle, Serama, Orloff, Ac, Aseel, Baheij, Bandara, and hybrids thereof.

Egg-laying chickens of the present disclosure include: Ameraucana, Ancona, Andalusian, Appenzeller, Araucana, Australorp, Barnevelder, Brahma, Buckeye, Buttercup, Campine, Catalana, Chantecler, Cochin, Cornish, Crevecoeur, Cubalaya, Deleware, Dominique, Dorking, Faverolles, Fayoumi, Hamburg, Holland, Houdan, Jaerhon, Java, Jersey Giant, La Fleche, Lakenvelder, Lamona, Langsham, Leghorn, Marans, Minorca, Nacked Neck, New Hampshire, Orloff, Orpington, Penedesenca, Phoenix, Plymouth Rock, Polish, Redcap, Rhode Island, Spanish, Sultan, Sussex, Welsumer, Wyandotte, Yokohama, and hybrids thereof.

While distinctions are made between broiler chickens and egg-laying chickens, embodiments of the present disclosure utilize broiler chickens, egg-laying chickens, and/or multipurpose chickens.

Chickens in commercial settings have been found to exhibit a high degree of bird-to-bird and location-to-location variability in terms of the microbial compositions of the gastrointestinal tract. While the increased hygiene of modern commercial hatcheries are thought to quell the bird losses, the increased hygiene may be contributing to the lack of colonization of the chicks/birds by maternally derived bacteria. The increased variability of the microbial compositions of the gastrointestinal tract of the birds in these facilities may lead to increased bird-to-bird and location-to-location variability that in turn results in a highly variable flock of birds with considerable differences in health, weight, and other attributes that affect commercial viability of the flock. The high variability amongst members of a single flock or even differences between locations impacts the susceptibility to pathogens, weight gain, and response to antibiotic treatment. See Stanley et al. (2013. PLOS ONE. 8(12):1-7; e84290).

In some embodiments, the administration of one or more microbes and/or bioensembles of the present disclosure early in a bird's life decreases the variability of the gut microbiome between birds and further establishes a stable gut microbiome.

In some embodiments, the variability of the gut microbiome is measured as the total number of species present in the gut at one or more locations. In some embodiments, the variability of the gut microbiome is measured as the presence or absence of particular taxa present in the gut at one or more locations. In some embodiments, the variability of the gut microbiome is measured as a difference in abundance of particular taxa present in the gut at one or more locations.

In some embodiments, the administration of one or more microbes and/or bioensembles of the present disclosure reduces the amount of time required for the gut microbiome to reach a stabilized state. In some embodiments, the administration of one or more microbes and/or bioensembles of the present disclosure reduces the amount of time required for the gut microbiome to reach a matured state.

In some embodiments, the administration of one or more microbes and/or bioensembles of the present disclosure results in poultry of the present disclosure reaching a stabilized state of the gut microbiome; a reduction in the variability of the gut microbiome.

In some embodiments, the stabilized state of the gut microbiome is reached when the gut microbiome of poultry contains about 10, about 20, about, 30, about 40, about 50, about 60, about 70, about 80, about 90, about 100, about 120, about 130, about 140, about 150, about 160, about 170, about 180, about 190, about 200, about 250, about 300, about 400, about 500, about 600, about 700, about 800, about 900, about 1,000, about 1,500, about 2,000, about 2,500, about 3,000, about 3,500, about 4,000, about 4,500, about 5,000, about 5,500, about 6,000, about 6,500, about 7,000, about 7,500, about 8,000, about 8,500, about 9,000, about 9,500, or about 10,000 different species.

In some embodiments, the stabilized state of the gut microbiome is reached when the gut microbiome of poultry contains between about 10 to about 50, about 10 to about 100, about 50 to about 100, about 50 to about 200, about 100 to about 150, about 100 to about 200, about 100 to about 400, about 200 to about 500, about 200 to about 700, about 400 to about 800, about 500 to about 1,000, about 500 to about 2,000, about 1,000 to about 2,000, about 1,000 to about 5,000, about 5,000 to about 7,000, about 5,000 to about 10,000, or about 8,000 to about 10,000 different species.

In some embodiments, at least 5%, at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, or at least 95% of the poultry in a pen/flock/hatchery reach a stabilized state after administration of one or more microbes and/or bioensembles of the present disclosure.

I. Competitive Exclusion and Immunomodulation

The ability of avian gut pathogens to adhere to a variety of molecules displayed in the glycocalyx/extracellular matrix of the avian gut is known to contribute to the pathogenicity of those particular organsisms/strains. See Martin and Smyth (2010. Anaerobe. 16:533-539) and Wade et al. (2016. Vet. Microbiol. 197:53-61). Microbes passed from adult poultry to hatchlings aid in protecting the hatchling during a vulnerable stage when the maternal antibodies and antimicrobial compounds (lysozymes among others) received from the egg white have depleted and the hatchling's immune system is not yet fully developed.

In some embodiments, the microbes and/or bioensembles of the present disclosure are producing the antimicrobial compounds. In some embodiments, the microbes and/or bioensembles are stimulating other microbes in the poultry to produce the antimicrobial compounds. In some embodiments, the microbes and/or bioensembles of the present disclosure are stimulating the immune system of the poultry, resulting in an increase in the production of antimicrobial compounds. In some embodiments, the antimicrobial compounds are produced in the gastrointestinal tract of the fowl and remain localized to the gastrointestinal tract. In some embodiments the antimicrobial compounds are produced distally from the gastrointestinal tract and localize to the gastrointestinal tract. In some embodiments, the antimicrobial compounds are circulated systemically in the poultry. In some aspects, the antimicrobial compounds include chemicals and compounds that are inhibitory, sporicidal, virucidal, bacteriostatic, or bacteriocidal to one or more microbes. In further embodiments, the antimicrobial compounds include chemicals and compounds that are inhibitory, sporicidal, virucidal, bacteriostatic, or bacteriocidal to one or more pathogenic microbes. In some embodiments, the antimicrobial compounds are as described throughout, and further including hydrogen peroxide, diacetyl, carbon dioxide, and bacteriocins (e.g., nisin, pediocin A, pediocin AcH, leucocin, helveticin J, and canobacteriocin). The antimicrobials presented herein are presented as exemplary antimicrobials and are not intented to limit the antimicrobials contemplated.

In some embodiments, the microbes and/or bioensemples of the present disclosure are administered to mature the gut/mucosal immune system more quickly than that of poultry that have not been administered the microbes and/or bioensembles. A mature gut/mucosal immune system is in contrast to a naïve gut/mucosal immune system, with regard to both adaptive immunity and innate immunity.

In some embodiments, microbes and bioensembles of the present disclosure are administered to competitively exclude microbial pathogens from causing a disease state in the poultry.

In some embodiments, microbes and bioensembles of the present disclosure competitively bind molecules of the glycocalyx/extracellular matrix of the gut cell walls to preclude or competitively inhibit pathogens from adhering to lectins and other molecules such as collagens (particularly types-III, IV, and V), gelatin, fibrinogen, laminin, and vitronectin. Pathogen adherence to these molecules are believed to contribute to the virulence of the pathogens.

In some embodiments, administration of microbial compositions of the present disclosure result in a decrease in the binding of pathogenic microbes to the glycocalyx/extracellular matrix of the cells of the poultry gastrointestinal tract.

In some embodiments, the microbial compositions of the present disclosure result in the binding of the administered microbes to the glycocalyx/extracellular matrix, preventing pathogenic microbes from adhering to the glycocalyx/extracellular matrix and preventing pathogenic disease.

In some embodiments, the microbial compositions of the present disclosure result in the chemical modification of the molecules of the glycocalyx/extracellular matrix by the administered microbial composition, preventing pathogenic microbes from adhering to the glycocalyx/extracellular matrix and preventing pathogenic disease.

In some embodiments, the molecules bound or chemically modified by the administered microbes are selected from lectins, collagens, gelatins, fibrinogens, laminins, and vitronectins.

In some embodiments, the gastrointestinal tract of poultry exhibit a decreased pH upon administration of one or more microbes and/or bioensembles of the present disclosure. The decreased pH may occur in the crop, proventriculus, gizzard/ventriculus, duodenum, small intestine, ceca, large intestine, or the cloaca.

In some embodiments, the gastrointestinal tract of poultry exhibit a decreased pH upon administration of one or more microbes and/or bioensembles of the present disclosure by at least 0.2, at least 0.4, at least 0.6, at least 0.8, at least 1, at least 1.2, at least 1.4, at least 1.6, at least 1.8, at least 2, at least 2.2, at least 2.4, at least 2.6, at least 2.8, at least 3, at least 3.2, at least 3.4, at least 3.6, at least 3.8, at least 4, at least 4.2, at least 4.4, at least 4.6, at least 4.8, at least 5, at least 5.2, at least 5.4, at least 5.6, at least 5.8, at least 6, at least 6.2, at least 6.4, at least 6.6, at least 6.8, or at least 7.

In some embodiments, the decrease in pH in the gastrointestinal tract of poultry prevents pathogenic microbes from outcompeting the non-pathogenic microbes in the gastrointestinal tract of poultry.

In some embodiments, the administration of microbial compositions of the present disclosure to poultry stimulate the production of B cells. In some embodiments, B cells are selected from regulatory B cells, B-1 cells, B-2 cells, marginal zone B cells, follicular B cells, memory B cells, plasma cells, and plasmablasts.

In some embodiments, the administration of microbial compositions of the present disclosure to poultry result in an increase of one or more types of B cells by at least 1%, at least 2%, at least 3%, at least 4%, at least 5%, at least 6%, at least 7%, at least 8%, at least 9%, at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95%.

In some embodiments, the administration of microbial composition of the present disclosure to poultry stimulate the production of T cells. In some embodiments, T cells are selected from γδ (gamma delta) T cells, αβ (alpha beta) T cells, natural killer T cells, regulatory T cells, memory T cells, cytotoxic T cells, helper T cells, and effector T cells.

In some embodiments, the administration of microbial compositions of the present disclosure to poultry result in an increase of one or more types of T cells by at least 1%, at least 2%, at least 3%, at least 4%, at least 5%, at least 6%, at least 7%, at least 8%, at least 9%, at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95%.

In some embodiments, the administration of microbial compositions of the present disclosure to poultry result in an increase in the number of isolated lymphoid follicles (ILFs).

In some embodiments, the administration of microbial compositions of the present disclosure to poultry result in an increase of isolated lymphoid follicles by at least 1%, at least 2%, at least 3%, at least 4%, at least 5%, at least 6%, at least 7%, at least 8%, at least 9%, at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95%.

In some embodiments, the administration of microbial compositions of the present disclosure result in the modulation of the gene expression of mucins, tight junction polypeptides, and cytokines. In some embodiments, the modulation of the gene expression of mucins, tight junction polypeptides, and cytokines results in an increase of the gene expression of said molecules. In some embodiments, the modulation of the gene expression of mucins, tight junction polypeptides, and cytokines results in a decrease of the gene expression of said molecules.

In some embodiments, the cytokines are selected from granulocyte-macrophage stimulating factor (GM-CSF), IL-1, IL-12, IL-18, tumor necrosis factor (TNF), and interferon gamma (IFN-γ). In some embodiments, the cytokines are selected from IL-4, IL-6, IL-10, IL-11, IL-13, and IL-1 receptor agonist.

In some embodiments, the administration of microbial compositions of the present disclosure result in a decrease of gut inflammation in poultry, as measured by the serum levels of inflammation markers. In some embodiment, the inflammation markers are selected from al-acid glycoprotein (AGP), IL-8, IL-1β, transforming growth factor (TGF-β4), and fatty acid-binding protein (FABP2).

In some embodiments, administration of the microbial compositions to egg-laying poultry results in an increase in the innate immune response in the resulting eggs of the egg-laying broilers. In some aspects, administration of the microbial compositions to the eggs of egg-laying poultry results in an increase in the innate immune response in the resulting eggs of the egg-laying poultry. In some aspects, administration of the microbial compositions to poultry results in an improvement in the innate immune response in the eggs of egg-laying poultry. The improvement or increase is measured against eggs/poultry that were not administered the microbial compositions. In some embodiments, the improvement or increase in the innate immune response in the eggs results in an increased hatching success, increased incidence of normal chick morphology, increased incidence of embryo survival, increased growth rate and total body mass in chicks.

In some embodiments, administration of the microbial compositions to egg-laying poultry or to eggs of egg-laying poultry results in either a decrease or an increase in egg-white proteins in the eggs.

In some embodiments, the innate immune response includes an improvement in the innate immune response in eggs of egg-laying poultry, the improvement is an increase or decrease in antimicrobials such as lysozyme, steroids, egg-white avidin, apoprotein, ovomucoid, ovomucin, ovoflavoprotein, ovoinhibitor, and conalbumin (ovotransferrin) in the egg. In some embodiments, the innate immune response includes an increase in antimicrobials such as lysozyme, steroids, egg-white avidin, apoprotein, ovomucoid, ovomucin, ovoflavoprotein, ovoinhibitor, and conalbumin (ovotransferrin). In some embodiments, administration of the microbial compositions to egg-laying poultry or to eggs of egg-laying poultry results in either a decrease or an increase in egg-white proteins, including lysozyme, steroids, egg-white avidin, apoprotein, ovomucoid, ovomucin, ovoflavoprotein, ovoinhibitor, and conalbumin (ovotransferrin).

In some embodiments, the administration of microbial compositions of the present disclosure to poultry or poultry eggs results in (1) an increase in hatching success, (2) an increase in the incidence of normal chick morphology, (3) an increase in the incidence of embryo survival, (4) an increase in chick growth rate and total body mass, wherein any one of the increases is an increase of at least 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% relative to poultry or poultry eggs not having been administered a microbial composition of the present disclosure.

In some embodiments, the administration of microbial compositions of the present disclosure to poultry or poultry eggs results in an increase in hatching success by at least 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% relative to poultry or poultry eggs not having been administered a microbial composition of the present disclosure.

In some embodiments, the administration of microbial compositions of the present disclosure to poultry or poultry eggs results in an increase in the incidence of normal chick morphology by at least 1%, 2%, 3%, 4%, 5%, 6%, 7% 8%, 9% 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% relative to poultry or poultry eggs not having been administered a microbial composition of the present disclosure.

In some embodiments, the administration of microbial compositions of the present disclosure to poultry or poultry eggs results in an increase in the incidence of embryo survival by at least 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% relative to poultry or poultry eggs not having been administered a microbial composition of the present disclosure.

In some embodiments, the administration of microbial compositions of the present disclosure to poultry or poultry eggs results in an increase in chick growth rate by at least 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% relative to poultry or poultry eggs not having been administered a microbial composition of the present disclosure.

In some embodiments, the administration of microbial compositions of the present disclosure to poultry or poultry eggs results in an increase in chick total body mass by at least 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% relative to poultry or poultry eggs not having been administered a microbial composition of the present disclosure.

In some embodiments, the administration of microbial compositions of the present disclosure to poultry or poultry eggs results in an increase or decrease in the concentration of lysozyme present in the egg by at least 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% relative to poultry or poultry eggs not having been administered a microbial composition of the present disclosure.

In some embodiments, the administration of microbial compositions of the present disclosure to poultry or poultry eggs results in an increase or decrease in the concentration of steroids present in the egg by at least 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% relative to poultry or poultry eggs not having been administered a microbial composition of the present disclosure.

In some embodiments, the administration of microbial compositions of the present disclosure to poultry or poultry eggs results in an increase or decrease in the concentration of avidin present in the egg by at least 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% relative to poultry or poultry eggs not having been administered a microbial composition of the present disclosure.

In some embodiments, the administration of microbial compositions of the present disclosure to poultry or poultry eggs results in an increase or decrease in the concentration of apoprotein present in the egg by at least 1%, 2%, 3%, 4%, 5%, 6%, 7% 8%, 9% 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% relative to poultry or poultry eggs not having been administered a microbial composition of the present disclosure.

In some embodiments, the administration of microbial compositions of the present disclosure to poultry or poultry eggs results in an increase or decrease in the concentration of ovomucoid present in the egg by at least 1%, 2%, 3% 4%, 5%, 6%, 7% 8%, 9% 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% relative to poultry or poultry eggs not having been administered a microbial composition of the present disclosure.

In some embodiments, the administration of microbial compositions of the present disclosure to poultry or poultry eggs results in an increase or decrease in the concentration of ovomucin present in the egg by at least 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% relative to poultry or poultry eggs not having been administered a microbial composition of the present disclosure.

In some embodiments, the administration of microbial compositions of the present disclosure to poultry or poultry eggs results in an increase or decrease in the concentration of ovoflavoprotein present in the egg by at least 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% relative to poultry or poultry eggs not having been administered a microbial composition of the present disclosure.

In some embodiments, the administration of microbial compositions of the present disclosure to poultry or poultry eggs results in an increase or decrease in the concentration of ovoinhibitor present in the egg by at least 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% relative to poultry or poultry eggs not having been administered a microbial composition of the present disclosure.

In some embodiments, the administration of microbial compositions of the present disclosure to poultry or poultry eggs results in an increase or decrease in the concentration of conalbumin present in the egg by at least 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% relative to poultry or poultry eggs not having been administered a microbial composition of the present disclosure.

Encapsulation Compositions

In some embodiments, the microbes or microbial compositions of the disclosure are encapsulated in an encapsulating composition. An encapsulating composition protects the microbes from external stressors prior to entering the gastrointestinal tract of poultry. In some embodiments, external stressors include thermal, desiccating, and physical stressors associated with pelleting and extrusion. In some embodiments, external stressors include chemicals present in the compositions to which Encapsulating compositions further create an environment that may be beneficial to the microbes, such as minimizing the oxidative stresses of an aerobic environment on anaerobic microbes, preserving the viability of the microbes wherein vegetative cells or spores form during the pelleting/extrusion process, etc. See Kalsta et al. (U.S. Pat. No. 5,104,662A), Ford (U.S. Pat. No. 5,733,568A), and Mosbach and Nilsson (U.S. Pat. No. 4,647,536A) for encapsulation compositions of microbes, and methods of encapsulating microbes.

In one embodiment, the compositions of the present disclosure exhibit a thermal tolerance, which is used interchangeably with heat tolerance and heat resistance. In one embodiment, thermal tolerant compositions of the present disclosure are tolerant of the high temperatures associated with feed manufacturing, mixing of feed and compositions of the present disclosure, storage in high heat environments, etc. In one embodiment, thermal tolerant compositions of the present disclosure are resistant to heat-killing and denaturation of the cell wall components and the intracellular environment. In one embodiment, the compositions of the present disclosure is tolerant or resistant to dessication/water loss.

In one embodiments, the encapsulation is a reservoir-type encapsulation. In one embodiment, the encapsulation is a matrix-type encapsulation. In one embodiment, the encapsulation is a coated matrix-type encapsulation. Burgain et al. (2011. J. Food Eng. 104:467-483) discloses numerous encapsulation embodiments and techniques, all of which are incorporated by reference.

In some embodiments, the compositions of the present disclosure are encapsulated in one or more of the following: gellan gum, xanthan gum, K-Carrageenan, cellulose acetate phthalate, chitosan, starch, milk fat, whey protein, Ca-alginate, raftilose, raftiline, pectin, saccharide, glucose, maltodextrin, gum arabic, guar, seed flour, alginate, dextrins, dextrans, celluloase, gelatin, gelatin, albumin, casein, gluten, acacia gum, tragacanth, wax, paraffin, stearic acid, monodiglycerides, and diglycerides. In some embodiments, the compositions of the present disclosure are encapsulated by one or more of a polymer, carbohydrate, sugar, plastic, glass, polysaccharide, lipid, wax, oil, fatty acid, or glyceride. In one embodiment, the microbial composition is encapsulated by a glucose. In one embodiment, the microbial composition is encapsulated by a glucose-containing composition. In one embodiment, formulations of the microbial composition comprise a glucose encapsulant. In one embodiment, formulations of the microbial composition comprise a glucose-encapsulated composition.

In some embodiments, the encapsulation of the compositions of the present disclosure is carried out by an extrusion, emulsification, coating, agglomeration, lyophilization, vacuum-drying, or spray-drying.

In one embodiment, the encapsulating composition comprises microcapsules having a multiplicity of liquid cores encapsulated in a solid shell material. For purposes of the disclosure, a “multiplicity” of cores is defined as two or more.

A first category of useful fusible shell materials is that of normally solid fats, including fats which are already of suitable hardness and animal or vegetable fats and oils which are hydrogenated until their melting points are sufficiently high to serve the purposes of the present disclosure. Depending on the desired process and storage temperatures and the specific material selected, a particular fat can be either a normally solid or normally liquid material. The terms “normally solid” and “normally liquid” as used herein refer to the state of a material at desired temperatures for storing the resulting microcapsules. Since fats and hydrogenated oils do not, strictly speaking, have melting points, the term “melting point” is used herein to describe the minimum temperature at which the fusible material becomes sufficiently softened or liquid to be successfully emulsified and spray cooled, thus roughly corresponding to the maximum temperature at which the shell material has sufficient integrity to prevent release of the choline cores. “Melting point” is similarly defined herein for other materials which do not have a sharp melting point.

Specific examples of fats and oils useful herein (some of which require hardening) are as follows: animal oils and fats, such as beef tallow, mutton tallow, lamb tallow, lard or pork fat, fish oil, and sperm oil; vegetable oils, such as canola oil, cottonseed oil, peanut oil, corn oil, olive oil, soybean oil, sunflower oil, safflower oil, coconut oil, palm oil, linseed oil, tung oil, and castor oil; fatty acid monoglycerides and diglycerides; free fatty acids, such as stearic acid, palmitic acid, and oleic acid; and mixtures thereof. The above listing of oils and fats is not meant to be exhaustive, but only exemplary.

Specific examples of fatty acids include linoleic acid, γ-linoleic acid, dihomo-γ-linolenic acid, arachidonic acid, docosatetraenoic acid, vaccenic acid, nervonic acid, mead acid, erucic acid, gondoic acid, elaidic acid, oleic acid, palitoleic acid, stearidonic acid, eicosapentaenoic acid, valeric acid, caproic acid, enanthic acid, caprylic acid, pelargonic acid, capric acid, undecylic acid, lauric acid, tridecylic acid, myristic acid, pentadecylic acid, palmitic acid, margaric acid, stearic acid, nonadecyclic acid, arachidic acid, heneicosylic acid, behenic acid, tricosylic acid, lignoceric acid, pentacosylic acid, cerotic acid, heptacosylic acid, montanic acid, nonacosylic acid, melissic acid, henatriacontylic acid, lacceroic acid, psyllic acid, geddic acid, ceroplastic acid, hexatriacontylic acid, heptatriacontanoic acid, and octatriacontanoic acid.

Another category of fusible materials useful as encapsulating shell materials is that of waxes. Representative waxes contemplated for use herein are as follows: animal waxes, such as beeswax, lanolin, shell wax, and Chinese insect wax; vegetable waxes, such as carnauba, candelilla, bayberry, and sugar cane; mineral waxes, such as paraffin, microcrystalline petroleum, ozocerite, ceresin, and montan; synthetic waxes, such as low molecular weight polyolefin (e.g., CARBOWAX), and polyol ether-esters (e.g., sorbitol); Fischer-Tropsch process synthetic waxes; and mixtures thereof. Water-soluble waxes, such as CARBOWAX and sorbitol, are not contemplated herein if the core is aqueous.

Still other fusible compounds useful herein are fusible natural resins, such as rosin, balsam, shellac, and mixtures thereof.

Various adjunct materials are contemplated for incorporation in fusible materials according to the present disclosure. For example, antioxidants, light stabilizers, dyes and lakes, flavors, essential oils, anti-caking agents, fillers, pH stabilizers, sugars (monosaccharides, disaccharides, trisaccharides, and polysaccharides) and the like can be incorporated in the fusible material in amounts which do not diminish its utility for the present disclosure.

The core material contemplated herein constitutes from about 0.1% to about 50%, about 1% to about 35%. or about 5% to about 30% by weight of the microcapsules. In some embodiments, the core material contemplated herein constitutes no more than about 30% by weight of the microcapsules. In some embodiments, the core material contemplated herein constitutes about 5% by weight of the microcapsules. The core material is contemplated as either a liquid or solid at contemplated storage temperatures of the microcapsules.

The cores may include other additives well-known in the pharmaceutical art, including edible sugars, such as sucrose, glucose, maltose, fructose, lactose, cellobiose, monosaccharides, disaccharides, trisaccharides, and polysaccharides, and mixtures thereof; artificial sweeteners, such as aspartame, saccharin, cyclamate salts, and mixtures thereof; edible acids, such as acetic acid (vinegar), citric acid, ascorbic acid, tartaric acid, and mixtures thereof; edible starches, such as corn starch; hydrolyzed vegetable protein; water-soluble vitamins, such as Vitamin C; water-soluble medicaments; water-soluble nutritional materials, such as ferrous sulfate; flavors; salts; monosodium glutamate; antimicrobial agents, such as sorbic acid; antimycotic agents, such as potassium sorbate, sorbic acid, sodium benzoate, and benzoic acid; food grade pigments and dyes; and mixtures thereof. Other potentially useful supplemental core materials will be apparent to those of ordinary skill in the art.

Emulsifying agents may be employed to assist in the formation of stable emulsions. Representative emulsifying agents include glyceryl monostearate, polysorbate esters, ethoxylated mono- and diglycerides, and mixtures thereof.

For ease of processing, and particularly to enable the successful formation of a reasonably stable emulsion, the viscosities of the core material and the shell material should be similar at the temperature at which the emulsion is formed. In particular, the ratio of the viscosity of the shell to the viscosity of the core, expressed in centipoise or comparable units, and both measured at the temperature of the emulsion, should be from about 22:1 to about 1:1, desirably from about 8:1 to about 1:1, and preferably from about 3:1 to about 1:1. A ratio of 1:1 would be ideal, but a viscosity ratio within the recited ranges is useful.

Encapsulating compositions are not limited to microcapsule compositions as disclosed above. In some embodiments encapsulating compositions encapsulate the microbial compositions in an adhesive polymer that can be natural or synthetic without toxic effect. In some embodiments, the encapsulating composition may be a matrix selected from sugar matrix, gelatin matrix, polymer matrix, silica matrix, starch matrix, foam matrix, glass/glassy matrix etc. See Pirzio et al. (U.S. Pat. No. 7,488,503). In some embodiments, the encapsulating composition may be selected from polyvinyl acetates; polyvinyl acetate copolymers; ethylene vinyl acetate (EVA) copolymers; polyvinyl alcohols; polyvinyl alcohol copolymers; celluloses, including ethylcelluloses, methylcelluloses, hydroxymethylcelluloses, hydroxypropylcelluloses and carboxymethylcellulose; polyvinylpyrolidones; polysaccharides, including starch, modified starch, dextrins, maltodextrins, alginate and chitosans; monosaccharides; fats; fatty acids, including oils; proteins, including gelatin and zeins; gum arabics; shellacs; vinylidene chloride and vinylidene chloride copolymers; calcium lignosulfonates; acrylic copolymers; polyvinylacrylates; polyethylene oxide; acrylamide polymers and copolymers; polyhydroxyethyl acrylate, methylacrylamide monomers; and polychloroprene.

In some embodiments, the microbial composition or a subcomponent thereof is encapsulated in a solid glass matrix or a flexible glass matrix (rubber matrix) comprising one or more polysaccharides, one or more saccharides, and/or one or more sugar alcohols. In some embodiments, the matrix comprises a monosaccharide or a disaccharide. In some embodiments, the disaccharide may be selected from sucrose, maltose, lactose, lactulose, trehalose, cellobiose, and chitobiose. In some embodiments, the polysaccharides, saccharides, and/or sugar alcohols are added to the microbial composition or a subcomponent thereof exogenously. In some embodiments, the matrix is an amorphous matrix. In some embodiments, the microbial composition or a subcomponent thereof is vitrified. In some embodiments, the microbial composition or a subcomponent thereof is desiccated. In some embodiments, the microbial composition or a subcomponent thereof is lyophilized. In some embodiments, the microbial composition or a subcomponent thereof is spray dried. In some embodiments, the microbial composition or a subcomponent thereof is spray congealed. In some embodiments, the microbial composition is preserved/stabilized by preservation by vaporization. See Harel and Kohavi-Beck (U.S. Pat. No. 8,097,245). See Bronshtein (U.S. Pat. No. 9,469,835).

In some embodiments, the encapsulating compositions comprise at least one layer of encapsulation. In some embodiments, the encapsulating compositions comprise at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, or at least 20 layers of encapsulation/encapsulants.

In some embodiments, the encapsulating compositions comprise at least two layers of encapsulation. In some embodiments, each layer of encapsulation confers a different characteristic to the composition. In some embodiments, no two consecutive layers confer the same characteristic. In some embodiments, at least one layer of the at least two layers of encapsulation confers thermostability, shelf stability, ultraviolet resistance, moisture resistance, dessication resistance, hydrophobicity, hydrophilicity, lipophobicity, lipophilicity, pH stability, acid resistance, and base resistance.

In some embodiments, the encapsulating compositions comprise two layers of encapsulation; the first layer confers thermostability and/or shelf stability, and the second layer provides pH resistance.

In some embodiments, the encapsulating layers confer a timed release of the microbial composition held in the center of the encapsulating layers. In some embodiments, the greater the number of layers confers a greater amount of time before the microbial composition is exposed, post administration.

In some embodiments, the encapsulating shell of the present disclosure can be up to 10 μm, 20 μm, 30 μm, 40 μm, 50 μm, 60 μm, 70 μm, 80 μm, 90 μm, 100 μm, 110 μm, 120 μm, 130 μm, 140 μm, 150 μm, 160 μm, 170 μm, 180 μm, 190 μm, 200 μm, 210 μm, 220 μm, 230 μm, 240 μm, 250 μm, 260 μm, 270 μm, 280 μm, 290 μm, 300 μm, 310 μm, 320 μm, 330 μm, 340 μm, 350 μm, 360 μm, 370 μm, 380 μm, 390 μm, 400 μm, 410 μm, 420 μm, 430 μm, 440 μm, 450 μm, 460 μm, 470 μm, 480 μm, 490 μm, 500 μm, 510 μm, 520 μm, 530 μm, 540 μm, 550 μm, 560 μm, 570 μm, 580 μm, 590 μm, 600 μm, 610 μm, 620 μm, 630 μm, 640 μm, 650 μm, 660 μm, 670 μm, 680 μm, 690 μm, 700 μm, 710 μm, 720 μm, 730 μm, 740 μm, 750 μm, 760 μm, 770 μm, 780 μm, 790 μm, 800 μm, 810 μm, 820 μm, 830 μm, 840 μm, 850 μm, 860 μm, 870 μm, 880 μm, 890 μm, 900 μm, 910 μm, 920 μm, 930 μm, 940 μm, 950 μm, 960 μm, 970 μm, 980 μm, 990 μm, 1000 μm, 1010 μm, 1020 μm, 1030 μm, 1040 μm, 1050 μm, 1060 μm, 1070 μm, 1080 μm, 1090 μm, 1100 μm, 1110 μm, 1120 μm, 1130 μm, 1140 μm, 1150 μm, 1160 μm, 1170 μm, 1180 μm, 1190 μm, 1200 μm, 1210 μm, 1220 μm, 1230 μm, 1240 μm, 1250 μm, 1260 μm, 1270 μm, 1280 μm, 1290 μm, 1300 μm, 1310 μm, 1320 μm, 1330 μm, 1340 μm, 1350 μm, 1360 μm, 1370 μm, 1380 μm, 1390 μm, 1400 μm, 1410 μm, 1420 μm, 1430 μm, 1440 μm, 1450 μm, 1460 μm, 1470 μm, 1480 μm, 1490 μm, 1500 μm, 1510 μm, 1520 μm, 1530 μm, 1540 μm, 1550 μm, 1560 μm, 1570 μm, 1580 μm, 1590 μm, 1600 μm, 1610 μm, 1620 μm, 1630 μm, 1640 μm, 1650 μm, 1660 μm, 1670 μm, 1680 μm, 1690 μm, 1700 μm, 1710 μm, 1720 μm, 1730 μm, 1740 μm, 1750 μm, 1760 μm, 1770 μm, 1780 μm, 1790 μm, 1800 μm, 1810 μm, 1820 μm, 1830 μm, 1840 μm, 1850 μm, 1860 μm, 1870 μm, 1880 μm, 1890 μm, 1900 μm, 1910 μm, 1920 μm, 1930 μm, 1940 μm, 1950 μm, 1960 μm, 1970 μm, 1980 μm, 1990 μm, 2000 μm, 2010 μm, 2020 μm, 2030 μm, 2040 μm, 2050 μm, 2060 μm, 2070 μm, 2080 μm, 2090 μm, 2100 μm, 2110 μm, 2120 μm, 2130 μm, 2140 μm, 2150 μm, 2160 μm, 2170 μm, 2180 μm, 2190 μm, 2200 μm, 2210 μm, 2220 μm, 2230 μm, 2240 μm, 2250 μm, 2260 μm, 2270 μm, 2280 μm, 2290 μm, 2300 μm, 2310 μm, 2320 μm, 2330 μm, 2340 μm, 2350 μm, 2360 μm, 2370 μm, 2380 μm, 2390 μm, 2400 μm, 2410 μm, 2420 μm, 2430 μm, 2440 μm, 2450 μm, 2460 μm, 2470 μm, 2480 μm, 2490 μm, 2500 μm, 2510 μm, 2520 μm, 2530 μm, 2540 μm, 2550 μm, 2560 μm, 2570 μm, 2580 μm, 2590 μm, 2600 μm, 2610 μm, 2620 μm, 2630 μm, 2640 μm, 2650 μm, 2660 μm, 2670 μm, 2680 μm, 2690 μm, 2700 μm, 2710 μm, 2720 μm, 2730 μm, 2740 μm, 2750 μm, 2760 μm, 2770 μm, 2780 μm, 2790 μm, 2800 μm, 2810 μm, 2820 μm, 2830 μm, 2840 μm, 2850 μm, 2860 μm, 2870 μm, 2880 μm, 2890 μm, 2900 μm, 2910 μm, 2920 μm, 2930 μm, 2940 μm, 2950 μm, 2960 μm, 2970 μm, 2980 μm, 2990 μm, or 3000 μm thick.

Animal Feed

In some embodiments, compositions of the present disclosure are mixed with animal feed. In some embodiments, animal feed may be present in various forms such as pellets, capsules, granulated, powdered, mash, liquid, or semi-liquid.

In some embodiments, compositions of the present disclosure are mixed into the premix or mash at the feed mill, alone as a standalone premix, and/or alongside other feed additives such as MONENSIN, vitamins, antibiotics, etc. In one embodiment, the compositions of the present disclosure are mixed into or onto the feed at the feed mill. In another embodiment, compositions of the present disclosure are mixed into the feed itself.

In some embodiments, feed of the present disclosure may be supplemented with water, premix or premixes, forage, fodder, beans (e.g., whole, cracked, or ground), grains (e.g., whole, cracked, or ground), bean- or grain-based oils, bean- or grain-based meals, bean- or grain-based haylage or silage, bean- or grain-based syrups, fatty acids, sugar alcohols (e.g., polyhydric alcohols), commercially available formula feeds, oyster shells and those of other bivalves, and mixtures thereof.

In some embodiments, forage encompasses hay, haylage, and silage. In some embodiments, hays include grass hays (e.g., sudangrass, orchardgrass, or the like), alfalfa hay, and clover hay. In some embodiments, haylages include grass haylages, sorghum haylage, and alfalfa haylage. In some embodiments, silages include maize, oat, wheat, alfalfa, clover, and the like.

In some embodiments, premix or premixes may be utilized in the feed. Premixes may comprise micro-ingredients such as vitamins, minerals, amino acids; chemical preservatives; pharmaceutical compositions such as antibiotics and other medicaments; fermentation products, and other ingredients. In some embodiments, premixes are blended into the feed.

In some embodiments, the feed may include feed concentrates such as soybean hulls, soybean oils, sugar beet pulp, molasses, high protein soybean meal, ground corn, shelled corn, wheat midds, distiller grain, cottonseed hulls, and grease. See Anderson et al. (U.S. Pat. No. 3,484,243), Iritani et al. (U.S. Pat. No. 6,090,416), Axelrod et al. (U.S. Publication US20060127530A1), and Katsumi et al. (U.S. Pat. No. 5,741,508) for animal feed and animal feed supplements capable of use in the present compositions and methods.

In some embodiments, feed occurs as a compound, which includes, in a mixed composition capable of meeting the basic dietary needs, the feed itself, vitamins, minerals, amino acids, and other necessary components. Compound feed may further comprise premixes.

In some embodiments, microbial compositions of the present disclosure may be mixed with animal feed, premix, and/or compound feed. Individual components of the animal feed may be mixed with the microbial compositions prior to feeding to poultry. The microbial compositions of the present disclosure may be applied into or on a premix, into or on a feed, and/or into or on a compound feed.

Administration of Microbial Compositions

In some embodiments, the microbial compositions of the present disclosure are administered to poultry via the oral route. In some embodiments the microbial compositions are administered via a direct injection route into the gastrointestinal tract. In further embodiments, the direct injection administration delivers the microbial compositions directly to one or more of the crop, gizzard, cecum, small intestine, and large intestine. FIG. 3 and FIG. 4 provide a detailed anatomical view of the gastrointestinal tract of a chicken. In some embodiments, the microbial compositions of the present disclosure are administered to animals through the cloaca. In further embodiments, cloacal administration is in the form of an inserted suppository.

In some embodiments, the microbial compositions are administered through drinking water, spraying on litter in which the animal is in contact with, mixing with medications or vaccines, and gavage. In some embodiments, the microbial compositions are sprayed directly on the animal, wherein the animal ingests the composition having been sprayed on the animal. In some embodiments, the microbial compositions are sprayed directly on the unhatched egg. In some embodiments, the microbial compositions are sprayed on and/or sprayed in feed, and the feed is administered to the animal. In further embodiments, the animal ingests the composition through the preening of feathers that have come into contact with the sprayed composition.

In some embodiments, the microbial compositions are mixed with the feed prior to administration. In some embodiments, the microbial compositions are pelleted with the feed prior to administration. In some embodiments, the microbial compositions are extruded with the feed prior to administration. In some aspects, the microbial compositions are mixed into the feed components as the feed is being prepared. In some aspects, a first group of one or more microbes of the microbial composition are pelleted with the feed, extruded with the feed, and/or mixed into the feed components as the feed is being prepared. In a further aspect, a second group of one or more microbes of the microbial composition are added to the feed which contains the first group of one or more microbes.

In some embodiments, the microbial compositions of the present disclosure are administered to poultry on day 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, or 31 post-hatching. In some embodiments, the microbial compositions are administered to the exterior surface of an egg as a liquid, semi-liquid, or solid on day 22, 21, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, 1, or 0 pre-hatching. In some embodiments, the microbial compositions of the present disclosure are administered to poultry in multiple dosing sessions in week(s) 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, and/or 30 week(s) post-hatching. In some embodiments, the microbial compositions are administered immediately after hatching. In some embodiments, the microbial compositions are administered into the egg (e.g., injection) by itself or administered along with other products such as vaccines. In some embodiments, the microbial compositions of the present disclosure are administered to poultry on hour 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, or 36 post-hatching.

In some embodiments, the microbial compositions are administered one or more times between the day of hatching and 5 days post-hatching, between the day of hatching and 10 days post-hatching, between the day of hatching and 14 days post-hatching, between the day of hatching and 16 days post-hatching, and between the day of hatching and 24 days post-hatching. In a further embodiment, a first microbial composition is administered one or more times between the day of hatching and 5 days post-hatching, between the day of hatching and 10 days post-hatching, between the day of hatching and 14 days post-hatching, between the day of hatching and 16 days post-hatching, and between the day of hatching and 24 days post-hatching.

In some embodiments, a first microbial composition is administered to poultry on day 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, or 31 post-hatching. In some embodiments, the first microbial composition is administered to the exterior surface of an egg as a liquid, semi-liquid, or solid on day 22, 21, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, 1, or 0 pre-hatching. In some embodiments, the first microbial composition of the present disclosure is administered to poultry in multiple dosing sessions in week(s) 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, and/or 30 week(s) post-hatching. In some embodiments, the first microbial composition is administered immediately after hatching. In some embodiments, the first microbial composition is administered into the egg (e.g., injection) by itself or administered along with other products such as vaccines. In some embodiments, the first microbial composition of the present disclosure is administered to poultry on hour 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, or 36 post-hatching.

In some embodiments, a second or subsequent microbial composition is administered to poultry on day 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, or 31 post-hatching. In some embodiments, a second or subsequent microbial composition is administered to the exterior surface of an egg as a liquid, semi-liquid, or solid on day 22, 21, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, 1, or 0 pre-hatching. In some embodiments, a second or subsequent microbial composition of the present disclosure is administered to poultry in multiple dosing sessions in week(s) 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, and/or 30 week(s) post-hatching. In some embodiments, a second or subsequent microbial composition is administered immediately after hatching. In some embodiments, a second or subsequent microbial composition is administered into the egg (e.g., injection) by itself or administered along with other products such as vaccines. In some embodiments, a second or subsequent microbial composition of the present disclosure is administered to poultry on hour 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, or 36 post-hatching

In some embodiments, the second or subsequent microbial composition is administered daily for the lifespan of the poultry. In some embodiments, the first microbial composition is administered daily for the lifespan of the poultry. In some embodiments, a microbial composition is administered daily for the lifespan of the poultry. In some embodiments, the poultry are administered a microbial composition comprising the same type or types of microbes for the duration of the poultry's life. In further embodiments, the microbial composition changes at at least once over the duration of the poultry's life, but the type or types of microbes in the microbial composition do not change.

In some embodiments, the subsequent microbial composition is a 3^(rd), 4^(th), 5^(th), 6^(th), 7^(th), 8^(th) 9^(th), or 10^(th) microbial composition, wherein the each of the microbial compositions are distinct from one another in the precise strains and/or microbes present in said compositions.

In some embodiments, the microbial composition is administered daily for the lifespan of the poultry. In some embodiments, the microbial composition is administered daily for the lifespan of the poultry beginning on day 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, or 31 post-hatching.

In some embodiments, the microbial composition is administered daily starting at day 1, 2, 3, 4, 5, 6, or 7 posthatching for the lifespan of the poultry. In some embodiments, the microbial composition is administered daily starting at day 4 or 5 posthatching for the lifespan of the poultry.

In some embodiments, the microbial composition is administered daily starting at day 1, 2, 3, 4, 5, 6, or 7 posthatching until the first feed change occurs. In some embodiments, the microbial composition is administered daily starting at day 4 or 5 until the first feed change occurs.

In some embodiments, a first microbial composition is administered daily starting at day 1, 2, 3, 4, 5, 6, or 7 posthatching until the first feed change occurs. In some embodiments, a second microbial composition is then administered daily beginning with the first feed change and spanning the lifespan of the poultry.

In some embodiments, the first microbial composition is administered daily starting at day 1, 2, 3, 4, 5, 6, or 7 posthatching until the first feed change occurs, and the second microbial composition is administered daily beginning on day 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 prior to the feed change occurs and continues for the lifespan of the poultry. In some embodiments, the first microbial composition is administered daily starting at day 1, 2, 3, 4, 5, 6, or 7 posthatching until the first feed change occurs, and the second microbial composition is administered daily beginning on day 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 after the feed change occurs and continues for the lifespan of the poultry.

In some embodiments, the microbial composition is administered daily for the lifespan of the poultry beginning on week 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 post-hatching. In some embodiments, the microbial composition is administered daily for the lifespan of the poultry beginning 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 week(s) prior to slaughter.

In some embodiments a different microbial composition is administered daily for the lifespan of the poultry beginning 1, 2, 3, 4, or 5 weeks prior to slaughter, and wherein this microbial composition is different from the first or second microbial compositions administered earlier in the life of the poultry.

In some embodiments, the first microbial administration is administered at least once daily until the first feed change occurs. In some embodiments, the first microbial administration is administered at least once weekly until the first feed change occurs. In some embodiments, the first microbial administration is administered at least twice daily until the first feed change occurs. In some embodiments, the first microbial administration is administered at least once daily for the life of the poultry. In some embodiments, the first microbial administration is administered at least once weekly for the life of the poultry. In some embodiments, the first microbial administration is administered at least twice daily for the life of the poultry.

In some embodiments, the second microbial administration is administered at least once daily beginning with the first feed change and spanning the lifespan of the poultry. In some embodiments, the second microbial administration is administered at least once weekly beginning with the first feed change and spanning the lifespan of the poultry. In some embodiments, the second microbial administration is administered at least twice daily beginning with the first feed change and spanning the lifespan of the poultry.

In some embodiments, the microbial composition is administered in a dose comprise a total of, or at least, 1 ml, 2 ml, 3 ml, 4 ml, 5 ml, 6 ml, 7 ml, 8 ml, 9 ml, 10 ml, 11 ml, 12 ml, 13 ml, 14 ml, 15 ml, 16 ml, 17 ml, 18 ml, 19 ml, 20 ml, 21 ml, 22 ml, 23 ml, 24 ml, 25 ml, 26 ml, 27 ml, 28 ml, 29 ml, 30 ml, 31 ml, 32 ml, 33 ml, 34 ml, 35 ml, 36 ml, 37 ml, 38 ml, 39 ml, 40 ml, 41 m, 42 ml, 43 ml, 44 ml, 45 ml, 46 ml, 47 ml, 48 ml, 49 ml, 50 ml, 60 ml, 70 ml, 80 ml, 90 ml, 100 ml, 200 ml, 300 ml, 400 ml, 500 ml, 600 ml, 700 ml, 800 ml, 900 ml, or 1,000 ml.

In some embodiments, the microbial composition is administered in a dose comprising a total of, or at least, 10¹⁸, 10¹⁷, 10¹⁶, 10¹⁵, 10¹⁴, 10¹³, 10¹², 10¹¹, 10¹⁰, 10⁹, 10⁸, 10⁷, 10⁶, 10⁵, 10⁴, 10³, or 10² microbial cells.

In some embodiments, the microbial compositions are mixed with feed, and the administration occurs through the ingestion of the microbial compositions along with the feed. In some embodiments, the dose of the microbial composition is administered such that there exists 10² to 10¹², 10³ to 10¹², 10⁴ to 10¹², 10⁵ to 10¹², 10⁶ to 10¹², 10⁷ to 10¹², 10⁸ to 10¹², 10⁹ to 10¹², 10¹⁰ to 10¹², 10¹¹ to 10¹², 10² to 10¹¹, 10³ to 10¹¹, 10⁴ to 10¹¹, 10⁵ to 10¹¹, 10⁶ to 10¹¹, 10⁷ to 10¹¹, 10⁸ to 10¹¹, 10⁹ to 10¹¹, 10¹⁰ to 10¹¹, 10² to 10¹⁰, 10³ to 10¹⁰, 10⁴ to 10¹⁰, 10⁵ to 10¹⁰, 10⁶ to 10¹⁰, 10⁷ to 10¹⁰, 10⁸ to 10¹⁰, 10⁹ to 10¹⁰, 10² to 10⁹, 10³ to 10⁹, 10⁴ to 10⁹, 10⁵ to 10⁹, 10⁶ to 10⁹, 10⁷ to 10⁹, 10¹ to 10⁹, 10² to 10⁸, 10³ to 10⁸, 10⁴ to 10⁸, 10⁵ to 10⁸, 10⁶ to 10⁸, 10⁷ to 10⁸, 10² to 10⁷, 10³ to 10⁷, 10⁴ to 10⁷, 10⁵ to 10⁷, 10⁶ to 10⁷, 10² to 10⁶, 10³ to 10⁶, 10⁴ to 10⁶, 10⁵ to 10⁶, 10² to 10⁵, 10³ to 10⁵, 10⁴ to 10⁵, 10² to 10⁴, 10³ to 10⁴, 10² to 10³, 10¹², 10¹¹, 10¹⁰, 10⁹, 10⁸, 10⁷, 10⁶, 10⁵, 10⁴, 10³, or 10² total microbial cells per gram or milliliter of the composition.

In some embodiments, the administered dose of the microbial composition comprises 10² to 10¹⁸, 10³ to 10¹⁸, 10⁴ to 10¹⁸, 10⁵ to 10¹⁸, 10⁶ to 10¹⁸, 10⁷ to 10¹⁸, 10⁸ to 10¹⁸, 10⁹ to 10¹⁸, 10¹⁰ to 10¹⁸, 10¹¹ to 10¹⁸, 10¹² to 10¹⁸, 10¹³ to 10¹⁸, 10¹⁴ to 10¹⁸, 10¹⁵ to 10¹⁸, 10¹⁶ to 10¹⁸, 10¹⁷ to 10¹⁸, 10² to 10¹², 10³ to 10¹², 10⁴ to 10¹², 10⁵ to 10¹², 10⁶ to 10¹², 10⁷ to 10¹², 10⁸ to 10¹², 10⁹ to 10¹², 10¹⁰ to 10¹², 10¹¹ to 10¹², 10² to 10¹¹, 10³ to 10¹¹, 10⁴ to 10¹¹, 10⁵ to 10¹¹, 10⁶ to 10¹¹, 10⁷ to 10¹¹, 10⁸ to 10¹¹, 10⁹ to 10¹¹, 10¹⁰ to 10¹¹, 10² to 10¹⁰, 10³ to 10¹⁰, 10⁴ to 10¹⁰, 10⁵ to 10¹⁰, 10⁶ to 10¹⁰, 10⁷ to 10¹⁰, 10⁸ to 10¹⁰, 10⁹ to 10¹⁰, 10² to 10⁹, 10³ to 10⁹, 10⁴ to 10⁹, 10⁵ to 10⁹, 10⁶ to 10⁹, 10⁷ to 10⁹, 10⁸ to 10⁹, 10² to 10⁸, 10³ to 10⁸, 10⁴ to 10⁸, 10⁵ to 10⁸, 10⁶ to 10⁸, 10⁷ to 10⁸, 10² to 10⁷, 10³ to 10⁷, 10⁴ to 10⁷, 10⁵ to 10⁷, 10⁶ to 10⁷, 10² to 10⁶, 10³ to 10⁶, 10⁴ to 10⁶, 10⁵ to 10⁶, 10² to 10⁵, 10³ to 10⁵, 10⁴ to 10⁵, 10² to 10⁴, 10³ to 10⁴, 10² to 10³, 10¹⁸, 10¹⁷, 10¹⁶, 10¹⁵, 10¹⁴, 10¹³, 10¹², 10¹¹, 10¹⁰, 10⁹, 10⁸, 10⁷, 10⁶, 10⁵, 10⁴, 10³, or 10² total microbial cells.

In some embodiments, the composition is administered 1 or more times per day. In some aspects, the composition is administered with food each time the animal is fed. In some embodiments, the composition is administered 1 to 10, 1 to 9, 1 to 8, 1 to 7, 1 to 6, 1 to 5, 1 to 4, 1 to 3, 1 to 2, 2 to 10, 2 to 9, 2 to 8, 2 to 7, 2 to 6, 2 to 5, 2 to 4, 2 to 3, 3 to 10, 3 to 9, 3 to 8, 3 to 7, 3 to 6, 3 to 5, 3 to 4, 4 to 10, 4 to 9, 4 to 8, 4 to 7, 4 to 6, 4 to 5, 5 to 10, 5 to 9, 5 to 8, 5 to 7, 5 to 6, 6 to 10, 6 to 9, 6 to 8, 6 to 7, 7 to 10, 7 to 9, 7 to 8, 8 to 10, 8 to 9, 9 to 10, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 times per day.

In some embodiments, the microbial composition is administered 1 to 10, 1 to 9, 1 to 8, 1 to 7, 1 to 6, 1 to 5, 1 to 4, 1 to 3, 1 to 2, 2 to 10, 2 to 9, 2 to 8, 2 to 7, 2 to 6, 2 to 5, 2 to 4, 2 to 3, 3 to 10, 3 to 9, 3 to 8, 3 to 7, 3 to 6, 3 to 5, 3 to 4, 4 to 10, 4 to 9, 4 to 8, 4 to 7, 4 to 6, 4 to 5, 5 to 10, 5 to 9, 5 to 8, 5 to 7, 5 to 6, 6 to 10, 6 to 9, 6 to 8, 6 to 7, 7 to 10, 7 to 9, 7 to 8, 8 to 10, 8 to 9, 9 to 10, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 times per week.

In some embodiments, the microbial composition is administered 1 to 10, 1 to 9, 1 to 8, 1 to 7, 1 to 6, 1 to 5, 1 to 4, 1 to 3, 1 to 2, 2 to 10, 2 to 9, 2 to 8, 2 to 7, 2 to 6, 2 to 5, 2 to 4, 2 to 3, 3 to 10, 3 to 9, 3 to 8, 3 to 7, 3 to 6, 3 to 5, 3 to 4, 4 to 10, 4 to 9, 4 to 8, 4 to 7, 4 to 6, 4 to 5, 5 to 10, 5 to 9, 5 to 8, 5 to 7, 5 to 6, 6 to 10, 6 to 9, 6 to 8, 6 to 7, 7 to 10, 7 to 9, 7 to 8, 8 to 10, 8 to 9, 9 to 10, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 times per month.

In some embodiments, the microbial composition is administered 1 to 10, 1 to 9, 1 to 8, 1 to 7, 1 to 6, 1 to 5, 1 to 4, 1 to 3, 1 to 2, 2 to 10, 2 to 9, 2 to 8, 2 to 7, 2 to 6, 2 to 5, 2 to 4, 2 to 3, 3 to 10, 3 to 9, 3 to 8, 3 to 7, 3 to 6, 3 to 5, 3 to 4, 4 to 10, 4 to 9, 4 to 8, 4 to 7, 4 to 6, 4 to 5, 5 to 10, 5 to 9, 5 to 8, 5 to 7, 5 to 6, 6 to 10, 6 to 9, 6 to 8, 6 to 7, 7 to 10, 7 to 9, 7 to 8, 8 to 10, 8 to 9, 9 to 10, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 times per year.

In some embodiments, the feed can be uniformly coated with one or more layers of the microbes and/or microbial compositions disclosed herein, using conventional methods of mixing, spraying, or a combination thereof through the use of treatment application equipment that is specifically designed and manufactured to accurately, safely, and efficiently apply coatings. Such equipment uses various types of coating technology such as rotary coaters, drum coaters, fluidized bed techniques, spouted beds, rotary mists, or a combination thereof. Liquid treatments such as those of the present disclosure can be applied via either a spinning “atomizer” disk or a spray nozzle, which evenly distributes the microbial composition onto the feed as it moves though the spray pattern. In some aspects, the feed is then mixed or tumbled for an additional period of time to achieve additional treatment distribution and drying.

In some embodiments, the feed coats of the present disclosure can be up to 10 μm, 20 μm, 30 μm, 40 μm, 50 μm, 60 μm, 70 μm, 80 μm, 90 μm, 100 μm, 110 μm, 120 μm, 130 μm, 140 μm, 150 μm, 160 μm, 170 μm, 180 μm, 190 μm, 200 μm, 210 μm, 220 μm, 230 μm, 240 μm, 250 μm, 260 μm, 270 μm, 280 μm, 290 μm, 300 μm, 310 μm, 320 μm, 330 μm, 340 μm, 350 μm, 360 μm, 370 μm, 380 μm, 390 μm, 400 μm, 410 μm, 420 μm, 430 μm, 440 μm, 450 μm, 460 μm, 470 μm, 480 μm, 490 μm, 500 μm, 510 μm, 520 μm, 530 μm, 540 μm, 550 μm, 560 μm, 570 μm, 580 μm, 590 μm, 600 μm, 610 μm, 620 μm, 630 μm, 640 μm, 650 μm, 660 μm, 670 μm, 680 μm, 690 μm, 700 μm, 710 μm, 720 μm, 730 μm, 740 μm, 750 μm, 760 μm, 770 μm, 780 μm, 790 μm, 800 μm, 810 μm, 820 μm, 830 μm, 840 μm, 850 μm, 860 μm, 870 μm, 880 μm, 890 μm, 900 μm, 910 μm, 920 μm, 930 μm, 940 μm, 950 μm, 960 μm, 970 μm, 980 μm, 990 μm, 1000 μm, 1010 μm, 1020 μm, 1030 μm, 1040 μm, 1050 μm, 1060 μm, 1070 μm, 1080 μm, 1090 μm, 1100 μm, 1110 μm, 1120 μm, 1130 μm, 1140 μm, 1150 μm, 1160 μm, 1170 μm, 1180 μm, 1190 μm, 1200 μm, 1210 μm, 1220 μm, 1230 μm, 1240 μm, 1250 μm, 1260 μm, 1270 μm, 1280 μm, 1290 μm, 1300 μm, 1310 μm, 1320 μm, 1330 μm, 1340 μm, 1350 μm, 1360 μm, 1370 μm, 1380 μm, 1390 μm, 1400 μm, 1410 μm, 1420 μm, 1430 μm, 1440 μm, 1450 μm, 1460 μm, 1470 μm, 1480 μm, 1490 μm, 1500 μm, 1510 μm, 1520 μm, 1530 μm, 1540 μm, 1550 μm, 1560 μm, 1570 μm, 1580 μm, 1590 μm, 1600 μm, 1610 μm, 1620 μm, 1630 μm, 1640 μm, 1650 μm, 1660 μm, 1670 μm, 1680 μm, 1690 μm, 1700 μm, 1710 μm, 1720 μm, 1730 μm, 1740 μm, 1750 μm, 1760 μm, 1770 μm, 1780 μm, 1790 μm, 1800 μm, 1810 μm, 1820 μm, 1830 μm, 1840 μm, 1850 μm, 1860 μm, 1870 μm, 1880 μm, 1890 μm, 1900 μm, 1910 μm, 1920 μm, 1930 μm, 1940 μm, 1950 μm, 1960 μm, 1970 μm, 1980 μm, 1990 μm, 2000 μm, 2010 μm, 2020 μm, 2030 μm, 2040 μm, 2050 μm, 2060 μm, 2070 μm, 2080 μm, 2090 μm, 2100 μm, 2110 μm, 2120 μm, 2130 μm, 2140 μm, 2150 μm, 2160 μm, 2170 μm, 2180 μm, 2190 μm, 2200 μm, 2210 μm, 2220 μm, 2230 μm, 2240 μm, 2250 μm, 2260 μm, 2270 μm, 2280 μm, 2290 μm, 2300 μm, 2310 μm, 2320 μm, 2330 μm, 2340 μm, 2350 μm, 2360 μm, 2370 μm, 2380 μm, 2390 μm, 2400 μm, 2410 μm, 2420 μm, 2430 μm, 2440 μm, 2450 μm, 2460 μm, 2470 μm, 2480 μm, 2490 μm, 2500 μm, 2510 μm, 2520 μm, 2530 μm, 2540 μm, 2550 μm, 2560 μm, 2570 μm, 2580 μm, 2590 μm, 2600 μm, 2610 μm, 2620 μm, 2630 μm, 2640 μm, 2650 μm, 2660 μm, 2670 μm, 2680 μm, 2690 μm, 2700 μm, 2710 μm, 2720 μm, 2730 μm, 2740 μm, 2750 μm, 2760 μm, 2770 μm, 2780 μm, 2790 μm, 2800 μm, 2810 μm, 2820 μm, 2830 μm, 2840 μm, 2850 μm, 2860 μm, 2870 μm, 2880 μm, 2890 μm, 2900 μm, 2910 μm, 2920 μm, 2930 μm, 2940 μm, 2950 μm, 2960 μm, 2970 μm, 2980 μm, 2990 μm, or 3000 μm thick.

In some embodiments, the microbial cells can be coated freely onto any number of compositions or they can be formulated in a liquid or solid composition before being coated onto a composition. For example, a solid composition comprising the microorganisms can be prepared by mixing a solid carrier with a suspension of spores or vegetative cells until the solid carriers are impregnated with the spore or cell suspension. This mixture can then be dried to obtain the desired particles.

In some other embodiments, it is contemplated that the solid or liquid microbial compositions of the present disclosure further contain functional agents e.g., activated carbon, minerals, vitamins, enzymes, antibiotics and/or other agents capable of improving the quality of the products or a combination thereof.

Methods of coating and compositions in use of said methods that are known in the art can be particularly useful when they are modified by the addition of one of the embodiments of the present disclosure. Such coating methods and apparatus for their application are disclosed in, for example: U.S. Pat. Nos. 8,097,245, 7,998,502, 9,044,497, 8,968,721, 9,737,578, 9,469,835, and 5,766,520; and PCT Pat. App. Publication Nos. WO 2008/076975, WO 2010/138522, WO2011/094469, WO 2010/111347, and WO 2010/111565, each of which is incorporated by reference herein.

In some embodiments, the microbes or microbial bioensembles of the present disclosure exhibit a synergistic effect, on one or more of the traits described herein, in the presence of one or more of the microbes or bioensembles coming into contact with one another. The synergistic effect obtained by the taught methods can be quantified, for example, according to Colby's formula (i.e., (E)=X+Y−(X*Y/100)). See Colby, R. S., “Calculating Synergistic and Antagonistic Responses of Herbicide Combinations,” 1967. Weeds. Vol. 15, pp. 20-22, incorporated herein by reference in its entirety. Thus, “synergistic” is intended to reflect an outcome/parameter/effect that has been increased by more than an additive amount.

In some embodiments, the microbes or microbial bioensembles of the present disclosure may be administered via drench. In one embodiment, the drench is an oral drench. A drench administration comprises utilizing a drench kit/applicator/syringe that injects/releases a liquid comprising the microbes or microbial bioensembles into the buccal cavity and/or esophagas of the animal.

In some embodiments, hatchlings/chicks are sprayed with microbial compositions of the present disclosure between day 0 and day 14 post hatching. In some embodiments, the microbial compositions of the present disclosure are administered to the poultry with food. In some embodiments, the spray-administered microbial composition comprises a different set of microbes than the microbial composition administered via food. In some embodiments, the spray-administered microbial composition and the microbial composition administered via food comprise the same set of microbes.

In some embodiments, the microbes or microbial bioensembles of the present disclosure may be administered in a time-released fashion. The composition may be coated in a chemical composition, or may be contained in a mechanical device or capsule that releases the microbes or microbial bioensembles over a period of time instead all at once. In one embodiment, the microbes or microbial bioensembles are administered to an animal in a time-release capsule. In one embodiment, the composition may be coated in a chemical composition, or may be contained in a mechanical device or capsule that releases the microbes or microbial bioensembles all at once a period of time hours post ingestion. In one embodiment, the composition may be coated in a chemical composition, or may be contained in a mechanical device or capsule that releases the microbes or microbial bioensembles at different locations within the gastrointestinal tract.

In some embodiments, the microbes or microbial bioensembles are administered in a time-released fashion between 1 to 5, 1 to 10, 1 to 15, 1 to 20, 1 to 24, 1 to 25, 1 to 30, 1 to 35, 1 to 40, 1 to 45, 1 to 50, 1 to 55, 1 to 60, 1 to 65, 1 to 70, 1 to 75, 1 to 80, 1 to 85, 1 to 90, 1 to 95, or 1 to 100 hours post administration of a time-release composition or device.

In some embodiments, the microbes or microbial bioensembles are administered in a time-released fashion between 1 to 2, 1 to 3, 1 to 4, 1 to 5, 1 to 6, 1 to 7, 1 to 8, 1 to 9, 1 to 10, 1 to 11, 1 to 12, 1 to 13, 1 to 14, 1 to 15, 1 to 16, 1 to 17, 1 to 18, 1 to 19, 1 to 20, 1 to 21, 1 to 22, 1 to 23, 1 to 24, 1 to 25, 1 to 26, 1 to 27, 1 to 28, 1 to 29, or 1 to 30 days post administration of a time-release composition or device.

Microorganisms

As used herein the term “microorganism” should be taken broadly. It includes, but is not limited to, the two prokaryotic domains, Bacteria and Archaea, as well as eukaryotic fungi, protists, and viruses.

By way of example, the microorganisms may include species of the genera of: Lactobacillus, Clostridium, Faecalibacter, Hydrogenoanaerobacterium, Acrocarpospora, Bacillus, Subdoligranulum, Leuconostoc, Lachnospira, Anaerofilum, Microbacterium, Verrucosispora, Blautia, Pseudomonas, Sporobacter, Corynebacterium Streptococcus, Paracoccus, Celulosilyticum, Ruminococcus, Bacteroides, Filobasidium, Gibberella, Alatospora, Pichia, and Candida. In some embodiments, the microorganisms may include species of any general disclosed herein.

In certain embodiments, the microorganism is unculturable. This should be taken to mean that the microorganism is not known to be culturable or is difficult to culture using methods known to one skilled in the art.

In one embodiment, the microbes are obtained from animals (e.g., mammals, reptiles, birds, and the like), soil (e.g., rhizosphere), air, water (e.g., marine, freshwater, wastewater sludge), sediment, oil, plants (e.g., roots, leaves, stems), agricultural products, and extreme environments (e.g., acid mine drainage or hydrothermal systems). In a further embodiment, microbes obtained from marine or freshwater environments such as an ocean, river, or lake. In a further embodiment, the microbes can be from the surface of the body of water, or any depth of the body of water (e.g., a deep sea sample).

The microorganisms of the disclosure may be isolated in substantially pure or mixed cultures. They may be concentrated, diluted, or provided in the natural concentrations in which they are found in the source material. For example, microorganisms from saline sediments may be isolated for use in this disclosure by suspending the sediment in fresh water and allowing the sediment to fall to the bottom. The water containing the bulk of the microorganisms may be removed by decantation after a suitable period of settling and either administered to the GI tract of poultry, or concentrated by filtering or centrifugation, diluted to an appropriate concentration and administered to the GI tract of poultry with the bulk of the salt removed. By way of further example, microorganisms from mineralized or toxic sources may be similarly treated to recover the microbes for application to poultry to minimize the potential for damage to the animal.

In another embodiment, the microorganisms are used in a crude form, in which they are not isolated from the source material in which they naturally reside. For example, the microorganisms are provided in combination with the source material in which they reside; for example, fecal matter or other composition found in the gastrointestinal tract. In this embodiment, the source material may include one or more species of microorganisms.

In some embodiments, a mixed population of microorganisms is used in the methods of the disclosure.

In embodiments of the disclosure where the microorganisms are isolated from a source material (for example, the material in which they naturally reside), any one or a combination of a number of standard techniques which will be readily known to skilled persons may be used. However, by way of example, these in general employ processes by which a solid or liquid culture of a single microorganism can be obtained in a substantially pure form, usually by physical separation on the surface of a solid microbial growth medium or by volumetric dilutive isolation into a liquid microbial growth medium. These processes may include isolation from dry material, liquid suspension, slurries or homogenates in which the material is spread in a thin layer over an appropriate solid gel growth medium, or serial dilutions of the material made into a sterile medium and inoculated into liquid or solid culture media.

Whilst not essential, in one embodiment, the material containing the microorganisms may be pre-treated prior to the isolation process in order to either multiply all microorganisms in the material. Microorganisms can then be isolated from the enriched materials as disclosed above.

In certain embodiments, as mentioned herein before, the microorganism(s) may be used in crude form and need not be isolated from an animal or a media. For example, feces, or growth media which includes the microorganisms identified to be of benefit to increased feed efficiency may be obtained and used as a crude source of microorganisms for the next round of the method or as a crude source of microorganisms at the conclusion of the method. For example, fresh feces could be obtained and optionally processed.

Microbiome Shift and Abundance of Microbes

In some embodiments, the microbiome of poultry, including the gut microbiome (crop, gizzard, cecum, small intestine, and large intestine) comprises a diverse environment of microbes with a wide variety of metabolic capabilities. The microbiome is influenced by a range of factors including diet, variations in animal metabolism, and breed, among others. Most poultry diets are plant-based and rich in complex polysaccharides that enrich the gastrointestinal microbial community for microbes capable of breaking down specific polymeric components in the diet such as cellulose, hemicellulose, lignin, etc. The end products of primary degradation sustain a chain of microbes that ultimately produce a range of organic acids together with hydrogen and carbon dioxide. Because of the complex and interlinked nature of the microbiome, changing the diet and thus substrates for primary degradation may have a cascading effect on gut microbial metabolism, with changes in both the organic acid profiles and the methane levels produced, thus impacting the quality and quantity of animal production and/or the products produced by the animal. See Menezes et al. (2011. FEMS Microbiol. Ecol. 78(2):256-265.)

In some aspects, the present disclosure is drawn to administering microbial compositions described herein to modulate or shift the microbiome of poultry.

In some embodiments, the microbiome is shifted through the administration of one or more microbes to the gastrointestinal tract. In further embodiments, the one or more microbes are those selected from Table 1 and/or Table 3. In some embodiments, the microbiome shift or modulation includes a decrease or loss of specific microbes that were present prior to the administration of one or more microbes of the present disclosure. In some embodiments, the microbiome shift or modulation includes an increase in microbes that were present prior to the administration of one or more microbes of the present disclosure. In some embodiments, the microbiome shift or modulation includes a gain of one or more microbes that were not present prior to the administration of one or more microbes of the present disclosure. In a further embodiment, the gain of one or more microbes is a microbe that was not specifically included in the administered microbial ensemble.

In some embodiments, the administration of microbes of the present disclosure results in a sustained modulation of the microbiome such that the administered microbes are present in the microbiome for a period of at least 1 to 10, 1 to 9, 1 to 8, 1 to 7, 1 to 6, 1 to 5, 1 to 4, 1 to 3, 1 to 2, 2 to 10, 2 to 9, 2 to 8, 2 to 7, 2 to 6, 2 to 5, 2 to 4, 2 to 3, 3 to 10, 3 to 9, 3 to 8, 3 to 7, 3 to 6, 3 to 5, 3 to 4, 4 to 10, 4 to 9, 4 to 8, 4 to 7, 4 to 6, 4 to 5, 5 to 10, 5 to 9, 5 to 8, 5 to 7, 5 to 6, 6 to 10, 6 to 9, 6 to 8, 6 to 7, 7 to 10, 7 to 9, 7 to 8, 8 to 10, 8 to 9, 9 to 10, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 days.

In some embodiments, the administration of microbes of the present disclosure results in a sustained modulation of the microbiome such that the administered microbes are present in the microbiome for a period of at least 1 to 10, 1 to 9, 1 to 8, 1 to 7, 1 to 6, 1 to 5, 1 to 4, 1 to 3, 1 to 2, 2 to 10, 2 to 9, 2 to 8, 2 to 7, 2 to 6, 2 to 5, 2 to 4, 2 to 3, 3 to 10, 3 to 9, 3 to 8, 3 to 7, 3 to 6, 3 to 5, 3 to 4, 4 to 10, 4 to 9, 4 to 8, 4 to 7, 4 to 6, 4 to 5, 5 to 10, 5 to 9, 5 to 8, 5 to 7, 5 to 6, 6 to 10, 6 to 9, 6 to 8, 6 to 7, 7 to 10, 7 to 9, 7 to 8, 8 to 10, 8 to 9, 9 to 10, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 weeks.

In some embodiments, the administration of microbes of the present disclosure results in a sustained modulation of the microbiome such that the administered microbes are present in the microbiome for a period of at least 1 to 10, 1 to 9, 1 to 8, 1 to 7, 1 to 6, 1 to 5, 1 to 4, 1 to 3, 1 to 2, 2 to 10, 2 to 9, 2 to 8, 2 to 7, 2 to 6, 2 to 5, 2 to 4, 2 to 3, 3 to 10, 3 to 9, 3 to 8, 3 to 7, 3 to 6, 3 to 5, 3 to 4, 4 to 10, 4 to 9, 4 to 8, 4 to 7, 4 to 6, 4 to 5, 5 to 10, 5 to 9, 5 to 8, 5 to 7, 5 to 6, 6 to 10, 6 to 9, 6 to 8, 6 to 7, 7 to 10, 7 to 9, 7 to 8, 8 to 10, 8 to 9, 9 to 10, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 months.

In some embodiments, the presence of the administered microbes are detected by sampling the gastrointestinal tract and using primers to amplify the 16S or 18S rDNA sequences, or the ITS rDNA sequences of the administered microbes. In some embodiments, the administered microbes are one or more of those selected from Table 1 and/or Table 3, and the corresponding rDNA sequences are those selected from SEQ ID NOs:1-387.

In some embodiments, the microbiome of a bird is measured by amplifying polynucleotides collected from gastrointestinal samples, wherein the polynucleotides may be 16S or 18S rDNA fragments, or ITS rDNA fragments of microbial rDNA. In one embodiment, the microbiome is fingerprinted by a method of denaturing gradient gel electrophoresis (DGGE) wherein the amplified rDNA fragments are sorted by where they denature, and form a unique banding pattern in a gel that may be used for comparing the microbiome of the same bird over time or the microbiomes of multiple birds. In another embodiment, the microbiome is fingerprinted by a method of terminal restriction fragment length polymorphism (T-RFLP), wherein labelled PCR fragments are digested using a restriction enzyme and then sorted by size. In a further embodiment, the data collected from the T-RFLP method is evaluated by nonmetric multidimensional scaling (nMDS) ordination and PERMANOVA statistics identify differences in microbiomes, thus allowing for the identification and measurement of shifts in the microbiome. See also Shanks et al. (2011. Appl. Environ. Microbiol. 77(9):2992-3001), Petri et al. (2013. PLOS one. 8(12):e83424), and Menezes et al. (2011. FEMS Microbiol. Ecol. 78(2):256-265.)

In some embodiments, the administration of microbes of the present disclosure results in a modulation or shift of the microbiome which further results in a desired phenotype or improved trait.

In some embodiments, the decrease in the variability of the number of unique species is a reduction of the total number of unique species of microbes in the small intestine to between 25 and 500, 25 and 400, 25 and 350, 25 and 300, 25 and 200, 25 and 100, 25 and 50, 50 and 500, 50 and 400, 50 and 300, 50 and 200, 50 and 100, 100 and 500, 100 and 400, 100 and 300, 100 and 200, 200 and 500, 200 and 400, 200 and 300, 300 and 500, 300 and 400, or 400 to 500 species.

MIC Scoring

According to the methods provided herein, a sample is processed to detect the presence of one or more microorganism types in the sample (FIG. 1, 1001 ; FIG. 2, 2001 ). The absolute number of one or more microorganism organism type in the sample is determined (FIG. 1, 1002 ; FIG. 2, 2002 ). The determination of the presence of the one or more organism types and the absolute number of at least one organism type can be conducted in parallel or serially. For example, in the case of a sample comprising a microbial community comprising bacteria (i.e., one microorganism type) and fungi (i.e., a second microorganism type), the user in one embodiment detects the presence of one or both of the organism types in the sample (FIG. 1, 1001 ; FIG. 2, 2001 ). The user, in a further embodiment, determines the absolute number of at least one organism type in the sample—in the case of this example, the number of bacteria, fungi or combination thereof, in the sample (FIG. 1, 1002 ; FIG. 2, 2002 ).

In one embodiment, the sample, or a portion thereof is subjected to flow cytometry (FC) analysis to detect the presence and/or number of one or more microorganism types (FIG. 1, 1001, 1002 ; FIG. 2, 2001, 2002 ). In one flow cytometer embodiment, individual microbial cells pass through an illumination zone, at a rate of at least about 300*s⁻¹, or at least about 500*s⁻¹, or at least about 1000*s⁻¹. However, one of ordinary skill in the art will recognize that this rate can vary depending on the type of instrument is employed. Detectors which are gated electronically measure the magnitude of a pulse representing the extent of light scattered. The magnitudes of these pulses are sorted electronically into “bins” or “channels,” permitting the display of histograms of the number of cells possessing a certain quantitative property (e.g., cell staining property, diameter, cell membrane) versus the channel number. Such analysis allows for the determination of the number of cells in each “bin” which in embodiments described herein is an “microorganism type” bin, e.g., a bacteria, fungi, nematode, protozoan, archaea, algae, dinoflagellate, virus, viroid, etc.

In one embodiment, a sample is stained with one or more fluorescent dyes wherein a fluorescent dye is specific to a particular microorganism type, to enable detection via a flow cytometer or some other detection and quantification method that harnesses fluorescence, such as fluorescence microscopy. The method can provide quantification of the number of cells and/or cell volume of a given organism type in a sample. In a further embodiment, as described herein, flow cytometry is harnessed to determine the presence and quantity of a unique first marker and/or unique second marker of the organism type, such as enzyme expression, cell surface protein expression, etc. Two- or three-variable histograms or contour plots of, for example, light scattering versus fluorescence from a cell membrane stain (versus fluorescence from a protein stain or DNA stain) may also be generated, and thus an impression may be gained of the distribution of a variety of properties of interest among the cells in the population as a whole. A number of displays of such multiparameter flow cytometric data are in common use and are amenable for use with the methods described herein.

In one embodiment of processing the sample to detect the presence and number of one or more microorganism types, a microscopy assay is employed (FIG. 1, 1001, 1002 ). In one embodiment, the microscopy is optical microscopy, where visible light and a system of lenses are used to magnify images of small samples. Digital images can be captured by a charge-couple device (CCD) camera. Other microscopic techniques include, but are not limited to, scanning electron microscopy and transmission electron microscopy. Microorganism types are visualized and quantified according to the aspects provided herein.

In another embodiment of in order to detect the presence and number of one or more microorganism types, the sample, or a portion thereof is subjected to fluorescence microscopy. Different fluorescent dyes can be used to directly stain cells in samples and to quantify total cell counts using an epifluorescence microscope as well as flow cytometry, described above. Useful dyes to quantify microorganisms include but are not limited to acridine orange (AO), 4,6-di-amino-2 phenylindole (DAPI) and 5-cyano-2,3 Dytolyl Tetrazolium Chloride (CTC). Viable cells can be estimated by a viability staining method such as the LIVE/DEAD® Bacterial Viability Kit (Bac-Light™) which contains two nucleic acid stains: the green-fluorescent SYTO 9™ dye penetrates all membranes and the red-fluorescent propidium iodide (PI) dye penetrates cells with damaged membranes. Therefore, cells with compromised membranes will stain red, whereas cells with undamaged membranes will stain green. Fluorescent in situ hybridization (FISH) extends epifluorescence microscopy, allowing for the fast detection and enumeration of specific organisms. FISH uses fluorescent labelled oligonucleotides probes (usually 15-25 basepairs) which bind specifically to organism DNA in the sample, allowing the visualization of the cells using an epifluorescence or confocal laser scanning microscope (CLSM). Catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) improves upon the FISH method by using oligonucleotide probes labelled with a horse radish peroxidase (HRP) to amplify the intensity of the signal obtained from the microorganisms being studied. FISH can be combined with other techniques to characterize microorganism communities. One combined technique is high affinity peptide nucleic acid (PNA)-FISH, where the probe has an enhanced capability to penetrate through the Extracellular Polymeric Substance (EPS) matrix. Another example is LIVE/DEAD-FISH which combines the cell viability kit with FISH and has been used to assess the efficiency of disinfection in drinking water distribution systems.

In another embodiment, the sample, or a portion thereof is subjected to Raman micro-spectroscopy in order to determine the presence of a microorganism type and the absolute number of at least one microorganism type (FIG. 1, 1001-1002 ; FIG. 2, 2001-2002 ). Raman micro-spectroscopy is a non-destructive and label-free technology capable of detecting and measuring a single cell Raman spectrum (SCRS). A typical SCRS provides an intrinsic biochemical “fingerprint” of a single cell. A SCRS contains rich information of the biomolecules within it, including nucleic acids, proteins, carbohydrates and lipids, which enables characterization of different cell species, physiological changes and cell phenotypes. Raman microscopy examines the scattering of laser light by the chemical bonds of different cell biomarkers. A SCRS is a sum of the spectra of all the biomolecules in one single cell, indicating a cell's phenotypic profile. Cellular phenotypes, as a consequence of gene expression, usually reflect genotypes. Thus, under identical growth conditions, different microorganism types give distinct SCRS corresponding to differences in their genotypes and can thus be identified by their Raman spectra.

In yet another embodiment, the sample, or a portion thereof is subjected to centrifugation in order to determine the presence of a microorganism type and the number of at least one microorganism type (FIG. 1, 1001-1002 ; FIG. 2, 2001-2002 ). This process sediments a heterogeneous mixture by using the centrifugal force created by a centrifuge. More dense components of the mixture migrate away from the axis of the centrifuge, while less dense components of the mixture migrate towards the axis. Centrifugation can allow fractionation of samples into cytoplasmic, membrane and extracellular portions. It can also be used to determine localization information for biological molecules of interest. Additionally, centrifugation can be used to fractionate total microbial community DNA. Different prokaryotic groups differ in their guanine-plus-cytosine (G+C) content of DNA, so density-gradient centrifugation based on G+C content is a method to differentiate organism types and the number of cells associated with each type. The technique generates a fractionated profile of the entire community DNA and indicates abundance of DNA as a function of G+C content. The total community DNA is physically separated into highly purified fractions, each representing a different G+C content that can be analyzed by additional molecular techniques such as denaturing gradient gel electrophoresis (DGGE)/amplified ribosomal DNA restriction analysis (ARDRA) (see discussion herein) to assess total microbial community diversity and the presence/quantity of one or more microorganism types.

In another embodiment, the sample, or a portion thereof is subjected to staining in order to determine the presence of a microorganism type and the number of at least one microorganism type (FIG. 1, 1001-1002 ; FIG. 2, 2001-2002 ). Stains and dyes can be used to visualize biological tissues, cells or organelles within cells. Staining can be used in conjunction with microscopy, flow cytometry or gel electrophoresis to visualize or mark cells or biological molecules that are unique to different microorganism types. In vivo staining is the process of dyeing living tissues, whereas in vitro staining involves dyeing cells or structures that have been removed from their biological context. Examples of specific staining techniques for use with the methods described herein include, but are not limited to: gram staining to determine gram status of bacteria, endospore staining to identify the presence of endospores, Ziehl-Neelsen staining, haematoxylin and eosin staining to examine thin sections of tissue, papanicolaou staining to examine cell samples from various bodily secretions, periodic acid-Schiff staining of carbohydrates, Masson's trichome employing a three-color staining protocol to distinguish cells from the surrounding connective tissue, Romanowsky stains (or common variants that include Wright's stain, Jenner's stain, May-Grunwald stain, Leishman stain and Giemsa stain) to examine blood or bone marrow samples, silver staining to reveal proteins and DNA, Sudan staining for lipids and Conklin's staining to detect true endospores. Common biological stains include acridine orange for cell cycle determination; bismarck brown for acid mucins; carmine for glycogen; carmine alum for nuclei; Coomassie blue for proteins; Cresyl violet for the acidic components of the neuronal cytoplasm; Crystal violet for cell walls; DAPI for nuclei; eosin for cytoplasmic material, cell membranes, some extracellular structures and red blood cells; ethidium bromide for DNA; acid fuchsine for collagen, smooth muscle or mitochondria; haematoxylin for nuclei; Hoechst stains for DNA; iodine for starch; malachite green for bacteria in the Gimenez staining technique and for spores; methyl green for chromatin; methylene blue for animal cells; neutral red for Nissl substance; Nile blue for nuclei; Nile red for lipohilic entities; osmium tetroxide for lipids; rhodamine is used in fluorescence microscopy; safranin for nuclei. Stains are also used in transmission electron microscopy to enhance contrast and include phosphotungstic acid, osmium tetroxide, ruthenium tetroxide, ammonium molybdate, cadmium iodide, carbohydrazide, ferric chloride, hexamine, indium trichloride, lanthanum nitrate, lead acetate, lead citrate, lead(II) nitrate, periodic acid, phosphomolybdic acid, potassium ferricyanide, potassium ferrocyanide, ruthenium red, silver nitrate, silver proteinate, sodium chloroaurate, thallium nitrate, thiosemicarbazide, uranyl acetate, uranyl nitrate, and vanadyl sulfate.

In another embodiment, the sample, or a portion thereof is subjected to mass spectrometry (MS) in order to determine the presence of a microorganism type and the number of at least one microorganism type (FIG. 1, 1001-1002 ; FIG. 2, 2001-2002 ). MS, as discussed below, can also be used to detect the presence and expression of one or more unique markers in a sample (FIG. 1, 1003-1004 ; FIG. 2, 2003-2004 ). MS is used for example, to detect the presence and quantity of protein and/or peptide markers unique to microorganism types and therefore to provide an assessment of the number of the respective microorganism type in the sample. Quantification can be either with stable isotope labelling or label-free. De novo sequencing of peptides can also occur directly from MS/MS spectra or sequence tagging (produce a short tag that can be matched against a database). MS can also reveal post-translational modifications of proteins and identify metabolites. MS can be used in conjunction with chromatographic and other separation techniques (such as gas chromatography, liquid chromatography, capillary electrophoresis, ion mobility) to enhance mass resolution and determination.

In another embodiment, the sample, or a portion thereof is subjected to lipid analysis in order to determine the presence of a microorganism type and the number of at least one microorganism type (FIG. 1, 1001-1002 ; FIG. 2, 2001-2002 ). Fatty acids are present in a relatively constant proportion of the cell biomass, and signature fatty acids exist in microbial cells that can differentiate microorganism types within a community. In one embodiment, fatty acids are extracted by saponification followed by derivatization to give the respective fatty acid methyl esters (FAMEs), which are then analyzed by gas chromatography. The FAME profile in one embodiment is then compared to a reference FAME database to identify the fatty acids and their corresponding microbial signatures by multivariate statistical analyses.

In the aspects of the methods provided herein, the number of unique first makers in the sample, or portion thereof (e.g., sample aliquot) is measured, as well as the abundance of each of the unique first markers (FIG. 1, 1003 ; FIG. 2, 2003 ). A unique marker is a marker of a microorganism strain. It should be understood by one of ordinary skill in the art that depending on the unique marker being probed for and measured, the entire sample need not be analyzed. For example, if the unique marker is unique to bacterial strains, then the fungal portion of the sample need not be analyzed. As described above, in some embodiments, measuring the absolute abundance of one or more organism types in a sample comprises separating the sample by organism type, e.g., via flow cytometry.

Any marker that is unique to an organism strain can be employed herein. For example, markers can include, but are not limited to, small subunit ribosomal RNA genes (16S/18S rDNA), large subunit ribosomal RNA genes (23S/25S/28S rDNA), intercalary 5.8S gene, cytochrome c oxidase, beta-tubulin, elongation factor, RNA polymerase and internal transcribed spacer (ITS).

Ribosomal RNA genes (rDNA), especially the small subunit ribosomal RNA genes, i.e., 18S rRNA genes (18S rDNA) in the case of eukaryotes and 16S rRNA (16S rDNA) in the case of prokaryotes, have been the predominant target for the assessment of organism types and strains in a microbial community. However, the large subunit ribosomal RNA genes, 28S rDNAs, have been also targeted. rDNAs are suitable for taxonomic identification because: (i) they are ubiquitous in all known organisms; (ii) they possess both conserved and variable regions; (iii) there is an exponentially expanding database of their sequences available for comparison. In community analysis of samples, the conserved regions serve as annealing sites for the corresponding universal PCR and/or sequencing primers, whereas the variable regions can be used for phylogenetic differentiation. In addition, the high copy number of rDNA in the cells facilitates detection from environmental samples.

The internal transcribed spacer (ITS), located between the 18S rDNA and 28S rDNA, has also been targeted. The ITS is transcribed but spliced away before assembly of the ribosomes The ITS region is composed of two highly variable spacers, ITS1 and ITS2, and the intercalary 5.8S gene. This rDNA operon occurs in multiple copies in genomes. Because the ITS region does not code for ribosome components, it is highly variable.

In one embodiment, the unique RNA marker can be an mRNA marker, an siRNA marker or a ribosomal RNA marker.

Protein-coding functional genes can also be used herein as a unique first marker. Such markers include but are not limited to: the recombinase A gene family (bacterial RecA, archaea RadA and RadB, eukaryotic Rad51 and Rad57, phage UvsX); RNA polymerase R subunit (RpoB) gene, which is responsible for transcription initiation and elongation; chaperonins. Candidate marker genes have also been identified for bacteria plus archaea: ribosomal protein S2 (rpsB), ribosomal protein S10 (rpsJ), ribosomal protein L1 (rplA), translation elongation factor EF-2, translation initiation factor IF-2, metalloendopeptidase, ribosomal protein L22, ffh signal recognition particle protein, ribosomal protein L4/L1e (rplD), ribosomal protein L2 (rplB), ribosomal protein S9 (rpsI), ribosomal protein L3 (rplC), phenylalanyl-tRNA synthetase beta subunit, ribosomal protein L14b/L23e (rplN), ribosomal protein S5, ribosomal protein S19 (rpsS), ribosomal protein S7, ribosomal protein L16/L10E (rplP), ribosomal protein S13 (rpsM), phenylalanyl-tRNA synthetase a subunit, ribosomal protein L15, ribosomal protein L25/L23, ribosomal protein L6 (rplF), ribosomal protein L11 (rplK), ribosomal protein L5 (rplE), ribosomal protein S12/S23, ribosomal protein L29, ribosomal protein S3 (rpsC), ribosomal protein S11 (rpsK), ribosomal protein L10, ribosomal protein S8, tRNA pseudouridine synthase B, ribosomal protein L18P/L5E, ribosomal protein S15P/S13e, Porphobilinogen deaminase, ribosomal protein S17, ribosomal protein L13 (rplM), phosphoribosylformylglycinamidine cyclo-ligase (rpsE), ribonuclease HII and ribosomal protein L24. Other candidate marker genes for bacteria include: transcription elongation protein NusA (nusA), rpoB DNA-directed RNA polymerase subunit beta (rpoB), GTP-binding protein EngA, rpoC DNA-directed RNA polymerase subunit beta′, priA primosome assembly protein, transcription-repair coupling factor, CTP synthase (pyrG), secY preprotein translocase subunit SecY, GTP-binding protein Obg/CgtA, DNA polymerase I, rpsF 30S ribosomal protein S6, poA DNA-directed RNA polymerase subunit alpha, peptide chain release factor 1, rplI 50S ribosomal protein L9, polyribonucleotide nucleotidyltransferase, tsf elongation factor Ts (tsf), rplQ 50S ribosomal protein L17, tRNA (guanine-N(1))-methyltransferase (rplS), rplY probable 50S ribosomal protein L25, DNA repair protein RadA, glucose-inhibited division protein A, ribosome-binding factor A, DNA mismatch repair protein MutL, smpB SsrA-binding protein (smpB), N-acetylglucosaminyl transferase, S-adenosyl-methyltransferase MraW, UDP-N-acetylmuramoylalanine-D-glutamate ligase, rplS 50S ribosomal protein L19, rplT 50S ribosomal protein L20 (rplT), ruvA Holliday junction DNA helicase, ruvB Holliday junction DNA helicase B, serS seryl-tRNA synthetase, rplU 50S ribosomal protein L21, rpsR 30S ribosomal protein S18, DNA mismatch repair protein MutS, rpsT 30S ribosomal protein S20, DNA repair protein RecN, frr ribosome recycling factor (frr), recombination protein RecR, protein of unknown function UPF0054, miaA tRNA isopentenyltransferase, GTP-binding protein YchF, chromosomal replication initiator protein DnaA, dephospho-CoA kinase, 16S rRNA processing protein RimM, ATP-cone domain protein, 1-deoxy-D-xylulose 5-phosphate reductoisomerase, 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase, fatty acid/phospholipid synthesis protein PlsX, tRNA(Ile)-lysidine synthetase, dnaG DNA primase (dnaG), ruvC Holliday junction resolvase, rpsP 30S ribosomal protein S16, Recombinase A recA, riboflavin biosynthesis protein RibF, glycyl-tRNA synthetase beta subunit, trmU tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase, rpmI 50S ribosomal protein L35, hemE uroporphyrinogen decarboxylase, Rod shape-determining protein, rpmA 50S ribosomal protein L27 (rpmA), peptidyl-tRNA hydrolase, translation initiation factor IF-3 (infC), UDP-N-acetylmuramyl-tripeptide synthetase, rpmF 50S ribosomal protein L32, rpIL 50S ribosomal protein L7/L12 (rpIL), leuS leucyl-tRNA synthetase, ligA NAD-dependent DNA ligase, cell division protein FtsA, GTP-binding protein TypA, ATP-dependent Clp protease, ATP-binding subunit ClpX, DNA replication and repair protein RecF and UDP-N-acetylenolpyruvoylglucosamine reductase.

Phospholipid fatty acids (PLFAs) may also be used as unique first markers according to the methods described herein. Because PLFAs are rapidly synthesized during microbial growth, are not found in storage molecules and degrade rapidly during cell death, it provides an accurate census of the current living community. All cells contain fatty acids (FAs) that can be extracted and esterified to form fatty acid methyl esters (FAMEs). When the FAMEs are analyzed using gas chromatography-mass spectrometry, the resulting profile constitutes a ‘fingerprint’ of the microorganisms in the sample. The chemical compositions of membranes for organisms in the domains Bacteria and Eukarya are comprised of fatty acids linked to the glycerol by an ester-type bond (phospholipid fatty acids (PLFAs)). In contrast, the membrane lipids of Archaea are composed of long and branched hydrocarbons that are joined to glycerol by an ether-type bond (phospholipid ether lipids (PLELs)). This is one of the most widely used non-genetic criteria to distinguish the three domains. In this context, the phospholipids derived from microbial cell membranes, characterized by different acyl chains, are excellent signature molecules, because such lipid structural diversity can be linked to specific microbial taxa.

As provided herein, in order to determine whether an organism strain is active, the level of expression of one or more unique second markers, which can be the same or different as the first marker, is measured (FIG. 1, 1004 ; FIG. 2, 2004 ). Unique first unique markers are described above. The unique second marker is a marker of microorganism activity. For example, in one embodiment, the mRNA or protein expression of any of the first markers described above is considered a unique second marker for the purposes of this invention.

In one embodiment, if the level of expression of the second marker is above a threshold level (e.g., a control level) or at a threshold level, the microorganism is considered to be active (FIG. 1, 1005 ; FIG. 2, 2005 ). Activity is determined in one embodiment, if the level of expression of the second marker is altered by at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, or at least about 30%, as compared to a threshold level, which in some embodiments, is a control level.

Second unique markers are measured, in one embodiment, at the protein, RNA or metabolite level. A unique second marker is the same or different as the first unique marker.

As provided above, a number of unique first markers and unique second markers can be detected according to the methods described herein. Moreover, the detection and quantification of a unique first marker is carried out according to methods known to those of ordinary skill in the art (FIG. 1, 1003-1004 , FIG. 2, 2003-2004 ).

Nucleic acid sequencing (e.g., gDNA, cDNA, rRNA, mRNA) in one embodiment is used to determine absolute abundance of a unique first marker and/or unique second marker. Sequencing platforms include, but are not limited to, Sanger sequencing and high-throughput sequencing methods available from Roche/454 Life Sciences, Illumina/Solexa, Pacific Biosciences, Ion Torrent and Nanopore. The sequencing can be amplicon sequencing of particular DNA or RNA sequences or whole metagenome/transcriptome shotgun sequencing.

Traditional Sanger sequencing (Sanger et al. (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl. Acad. Sci. USA, 74, pp. 5463-5467, incorporated by reference herein in its entirety) relies on the selective incorporation of chain-terminating dideoxynucleotides by DNA polymerase during in vitro DNA replication and is amenable for use with the methods described herein.

In another embodiment, the sample, or a portion thereof is subjected to extraction of nucleic acids, amplification of DNA of interest (such as the rRNA gene) with suitable primers and the construction of clone libraries using sequencing vectors. Selected clones are then sequenced by Sanger sequencing and the nucleotide sequence of the DNA of interest is retrieved, allowing calculation of the number of unique microorganism strains in a sample.

454 pyrosequencing from Roche/454 Life Sciences yields long reads and can be harnessed in the methods described herein (Margulies et al. (2005) Nature, 437, pp. 376-380; U.S. Pat. Nos. 6,274,320; 6,258,568; 6,210,891, each of which is herein incorporated in its entirety for all purposes). Nucleic acid to be sequenced (e.g., amplicons or nebulized genomic/metagenomic DNA) have specific adapters affixed on either end by PCR or by ligation. The DNA with adapters is fixed to tiny beads (ideally, one bead will have one DNA fragment) that are suspended in a water-in-oil emulsion. An emulsion PCR step is then performed to make multiple copies of each DNA fragment, resulting in a set of beads in which each bead contains many cloned copies of the same DNA fragment. Each bead is then placed into a well of a fiber-optic chip that also contains enzymes necessary for the sequencing-by-synthesis reactions. The addition of bases (such as A, C, G, or T) trigger pyrophosphate release, which produces flashes of light that are recorded to infer the sequence of the DNA fragments in each well. About 1 million reads per run with reads up to 1,000 bases in length can be achieved. Paired-end sequencing can be done, which produces pairs of reads, each of which begins at one end of a given DNA fragment. A molecular barcode can be created and placed between the adapter sequence and the sequence of interest in multiplex reactions, allowing each sequence to be assigned to a sample bioinformatically.

Illumina/Solexa sequencing produces average read lengths of about 25 basepairs (bp) to about 300 bp (Bennett et al. (2005) Pharmacogenomics, 6:373-382; Lange et al. (2014). BMC Genomics 15, p. 63; Fadrosh et al. (2014) Microbiome 2, p. 6; Caporaso et al. (2012) ISME J, 6, p. 1621-1624; Bentley et al. (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature, 456:53-59). This sequencing technology is also sequencing-by-synthesis but employs reversible dye terminators and a flow cell with a field of oligos attached. DNA fragments to be sequenced have specific adapters on either end and are washed over a flow cell filled with specific oligonucleotides that hybridize to the ends of the fragments. Each fragment is then replicated to make a cluster of identical fragments. Reversible dye-terminator nucleotides are then washed over the flow cell and given time to attach. The excess nucleotides are washed away, the flow cell is imaged, and the reversible terminators can be removed so that the process can repeat and nucleotides can continue to be added in subsequent cycles. Paired-end reads that are 300 bases in length each can be achieved. An Illumina platform can produce 4 billion fragments in a paired-end fashion with 125 bases for each read in a single run. Barcodes can also be used for sample multiplexing, but indexing primers are used.

The SOLiD (Sequencing by Oligonucleotide Ligation and Detection, Life Technologies) process is a “sequencing-by-ligation” approach, and can be used with the methods described herein for detecting the presence and abundance of a first marker and/or a second marker (FIG. 1, 1003-1004 ; FIG. 2, 2003-2004 ) (Peckham et al. SOLiD™ Sequencing and 2-Base Encoding. San Diego, Calif.: American Society of Human Genetics, 2007; Mitra et al. (2013) Analysis of the intestinal microbiota using SOLiD 16S rRNA gene sequencing and SOLiD shotgun sequencing. BMC Genomics, 14(Suppl 5): S16; Mardis (2008) Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet, 9:387-402; each incorporated by reference herein in its entirety). A library of DNA fragments is prepared from the sample to be sequenced, and are used to prepare clonal bead populations, where only one species of fragment will be present on the surface of each magnetic bead. The fragments attached to the magnetic beads will have a universal P1 adapter sequence so that the starting sequence of every fragment is both known and identical. Primers hybridize to the P1 adapter sequence within the library template. A set of four fluorescently labelled di-base probes compete for ligation to the sequencing primer. Specificity of the di-base probe is achieved by interrogating every 1st and 2nd base in each ligation reaction. Multiple cycles of ligation, detection and cleavage are performed with the number of cycles determining the eventual read length. The SOLiD platform can produce up to 3 billion reads per run with reads that are 75 bases long. Paired-end sequencing is available and can be used herein, but with the second read in the pair being only 35 bases long. Multiplexing of samples is possible through a system akin to the one used by Illumina, with a separate indexing run.

The Ion Torrent system, like 454 sequencing, is amenable for use with the methods described herein for detecting the presence and abundance of a first marker and/or a second marker (FIG. 1, 1003-1004 ; FIG. 2, 2003-2004 ). It uses a plate of microwells containing beads to which DNA fragments are attached. It differs from all of the other systems, however, in the manner in which base incorporation is detected. When a base is added to a growing DNA strand, a proton is released, which slightly alters the surrounding pH. Microdetectors sensitive to pH are associated with the wells on the plate, and they record when these changes occur. The different bases (A, C, G, T) are washed sequentially through the wells, allowing the sequence from each well to be inferred. The Ion Proton platform can produce up to 50 million reads per run that have read lengths of 200 bases. The Personal Genome Machine platform has longer reads at 400 bases. Bidirectional sequencing is available. Multiplexing is possible through the standard in-line molecular barcode sequencing.

Pacific Biosciences (PacBio) SMRT sequencing uses a single-molecule, real-time sequencing approach and in one embodiment, is used with the methods described herein for detecting the presence and abundance of a first marker and/or a second marker (FIG. 1, 1003-1004 ; FIG. 2, 2003-2004 ). The PacBio sequencing system involves no amplification step, setting it apart from the other major next-generation sequencing systems. In one embodiment, the sequencing is performed on a chip containing many zero-mode waveguide (ZMW) detectors. DNA polymerases are attached to the ZMW detectors and phospholinked dye-labeled nucleotide incorporation is imaged in real time as DNA strands are synthesized. The PacBio system yields very long read lengths (averaging around 4,600 bases) and a very high number of reads per run (about 47,000). The typical “paired-end” approach is not used with PacBio, since reads are typically long enough that fragments, through CCS, can be covered multiple times without having to sequence from each end independently. Multiplexing with PacBio does not involve an independent read, but rather follows the standard “in-line” barcoding model.

In one embodiment, where the first unique marker is the ITS genomic region, automated ribosomal intergenic spacer analysis (ARISA) is used in one embodiment to determine the number and identity of microorganism strains in a sample (FIG. 1, 1003 , FIG. 2, 2003 ) (Ranjard et al. (2003). Environmental Microbiology 5, pp. 1111-1120, incorporated by reference in its entirety for all puposes). The ITS region has significant heterogeneity in both length and nucleotide sequence. The use of a fluorescence-labeled forward primer and an automatic DNA sequencer permits high resolution of separation and high throughput. The inclusion of an internal standard in each sample provides accuracy in sizing general fragments.

In another embodiment, fragment length polymorphism (RFLP) of PCR-amplified rDNA fragments, otherwise known as amplified ribosomal DNA restriction analysis (ARDRA), is used to characterize unique first markers and the abundance of the same in samples (FIG. 1, 1003 , FIG. 2, 2003 ) (Massol-Deya et al. (1995). Mol. Microb. Ecol. Manual. 3.3.2, pp. 1-18, incorporated by reference in its entirety for all puposes). rDNA fragments are generated by PCR using general primers, digested with restriction enzymes, electrophoresed in agarose or acrylamide gels, and stained with ethidium bromide or silver nitrate.

One fingerprinting technique used in detecting the presence and abundance of a unique first marker is single-stranded-conformation polymorphism (SSCP) (Lee et al. (1996). Appl Environ Microbiol 62, pp. 3112-3120; Scheinert et al. (1996). J. Microbiol. Methods 26, pp. 103-117; Schwieger and Tebbe (1998). Appl. Environ. Microbiol. 64, pp. 4870-4876, each of which is incorporated by reference herein in its entirety). In this technique, DNA fragments such as PCR products obtained with primers specific for the 16S rRNA gene, are denatured and directly electrophoresed on a non-denaturing gel. Separation is based on differences in size and in the folded conformation of single-stranded DNA, which influences the electrophoretic mobility. Reannealing of DNA strands during electrophoresis can be prevented by a number of strategies, including the use of one phosphorylated primer in the PCR followed by specific digestion of the phosphorylated strands with lambda exonuclease and the use of one biotinylated primer to perform magnetic separation of one single strand after denaturation. To assess the identity of the predominant populations in a given bioensemble, in one embodiment, bands are excised and sequenced, or SSCP-patterns can be hybridized with specific probes. Electrophoretic conditions, such as gel matrix, temperature, and addition of glycerol to the gel, can influence the separation.

In addition to sequencing based methods, other methods for quantifying expression (e.g., gene, protein expression) of a second marker are amenable for use with the methods provided herein for determining the level of expression of one or more second markers (FIG. 1, 1004 ; FIG. 2, 2004 ). For example, quantitative RT-PCR, microarray analysis, linear amplification techniques such as nucleic acid sequence based amplification (NASBA) are all amenable for use with the methods described herein, and can be carried out according to methods known to those of ordinary skill in the art.

In another embodiment, the sample, or a portion thereof is subjected to a quantitative polymerase chain reaction (PCR) for detecting the presence and abundance of a first marker and/or a second marker (FIG. 1, 1003-1004 ; FIG. 2, 2003-2004 ). Specific microorganism strains activity is measured by reverse transcription of transcribed ribosomal and/or messenger RNA (rRNA and mRNA) into complementary DNA (cDNA), followed by PCR (RT-PCR).

In another embodiment, the sample, or a portion thereof is subjected to PCR-based fingerprinting techniques to detect the presence and abundance of a first marker and/or a second marker (FIG. 1, 1003-1004 ; FIG. 2, 2003-2004 ). PCR products can be separated by electrophoresis based on the nucleotide composition. Sequence variation among the different DNA molecules influences the melting behaviour, and therefore molecules with different sequences will stop migrating at different positions in the gel. Thus electrophoretic profiles can be defined by the position and the relative intensity of different bands or peaks and can be translated to numerical data for calculation of diversity indices. Bands can also be excised from the gel and subsequently sequenced to reveal the phylogenetic affiliation of the community members. Electrophoresis methods include, but are not limited to: denaturing gradient gel electrophoresis (DGGE), temperature gradient gel electrophoresis (TGGE), single-stranded-conformation polymorphism (SSCP), restriction fragment length polymorphism analysis (RFLP) or amplified ribosomal DNA restriction analysis (ARDRA), terminal restriction fragment length polymorphism analysis (T-RFLP), automated ribosomal intergenic spacer analysis (ARISA), randomly amplified polymorphic DNA (RAPD), DNA amplification fingerprinting (DAF) and Bb-PEG electrophoresis.

In another embodiment, the sample, or a portion thereof is subjected to a chip-based platform such as microarray or microfluidics to determine the abundance of a unique first marker and/or presence/abundance of a unique second marker (FIG. 1, 1003-1004 , FIG. 2, 2003-2004 ). The PCR products are amplified from total DNA in the sample and directly hybridized to known molecular probes affixed to microarrays. After the fluorescently labeled PCR amplicons are hybridized to the probes, positive signals are scored by the use of confocal laser scanning microscopy. The microarray technique allows samples to be rapidly evaluated with replication, which is a significant advantage in microbial community analyses. In general, the hybridization signal intensity on microarrays is directly proportional to the abundance of the target organism. The universal high-density 16S microarray (PhyloChip) contains about 30,000 probes of 16SrRNA gene targeted to several cultured microbial species and “candidate divisions”. These probes target all 121 demarcated prokaryotic orders and allow simultaneous detection of 8,741 bacterial and archaeal taxa. Another microarray in use for profiling microbial communities is the Functional Gene Array (FGA). Unlike PhyloChips, FGAs are designed primarily to detect specific metabolic groups of bacteria. Thus, FGA not only reveal the community structure, but they also shed light on the in situ community metabolic potential. FGA contain probes from genes with known biological functions, so they are useful in linking microbial community composition to ecosystem functions. An FGA termed GeoChip contains >24,000 probes from all known metabolic genes involved in various biogeochemical, ecological, and environmental processes such as ammonia oxidation, methane oxidation, and nitrogen fixation.

A protein expression assay, in one embodiment, is used with the methods described herein for determining the level of expression of one or more second markers (FIG. 1, 1004 ; FIG. 2, 2004 ). For example, in one embodiment, mass spectrometry or an immunoassay such as an enzyme-linked immunosorbant assay (ELISA) is utilized to quantify the level of expression of one or more unique second markers, wherein the one or more unique second markers is a protein.

In one embodiment, the sample, or a portion thereof is subjected to Bromodeoxyuridine (BrdU) incorporation to determine the level of a second unique marker (FIG. 1, 1004 ; FIG. 2, 2004 ). BrdU, a synthetic nucleoside analog of thymidine, can be incorporated into newly synthesized DNA of replicating cells. Antibodies specific for BRdU can then be used for detection of the base analog. Thus BrdU incorporation identifies cells that are actively replicating their DNA, a measure of activity of a microorganism according to one embodiment of the methods described herein. BrdU incorporation can be used in combination with FISH to provide the identity and activity of targeted cells.

In one embodiment, the sample, or a portion thereof is subjected to microautoradiography (MAR) combined with FISH to determine the level of a second unique marker (FIG. 1, 1004 ; FIG. 2, 2004 ). MAR-FISH is based on the incorporation of radioactive substrate into cells, detection of the active cells using autoradiography and identification of the cells using FISH. The detection and identification of active cells at single-cell resolution is performed with a microscope. MAR-FISH provides information on total cells, probe targeted cells and the percentage of cells that incorporate a given radiolabelled substance. The method provides an assessment of the in situ function of targeted microorganisms and is an effective approach to study the in vivo physiology of microorganisms. A technique developed for quantification of cell-specific substrate uptake in combination with MAR-FISH is known as quantitative MAR (QMAR).

In one embodiment, the sample, or a portion thereof is subjected to stable isotope Raman spectroscopy combined with FISH (Raman-FISH) to determine the level of a second unique marker (FIG. 1, 1004 ; FIG. 2, 2004 ). This technique combines stable isotope probing, Raman spectroscopy and FISH to link metabolic processes with particular organisms. The proportion of stable isotope incorporation by cells affects the light scatter, resulting in measurable peak shifts for labelled cellular components, including protein and mRNA components. Raman spectroscopy can be used to identify whether a cell synthesizes compounds including, but not limited to: oil (such as alkanes), lipids (such as triacylglycerols (TAG)), specific proteins (such as heme proteins, metalloproteins), cytochrome (such as P450, cytochrome c), chlorophyll, chromophores (such as pigments for light harvesting carotenoids and rhodopsins), organic polymers (such as polyhydroxyalkanoates (PHA), polyhydroxybutyrate (PHB)), hopanoids, steroids, starch, sulfide, sulfate and secondary metabolites (such as vitamin B12).

In one embodiment, the sample, or a portion thereof is subjected to DNA/RNA stable isotope probing (SIP) to determine the level of a second unique marker (FIG. 1, 1004 ; FIG. 2, 2004 ). SIP enables determination of the microbial diversity associated with specific metabolic pathways and has been generally applied to study microorganisms involved in the utilization of carbon and nitrogen compounds. The substrate of interest is labelled with stable isotopes (such as 13C or ¹⁵N) and added to the sample. Only microorganisms able to metabolize the substrate will incorporate it into their cells. Subsequently, ¹³C-DNA and ¹⁵N-DNA can be isolated by density gradient centrifugation and used for metagenomic analysis. RNA-based SIP can be a responsive biomarker for use in SIP studies, since RNA itself is a reflection of cellular activity.

In one embodiment, the sample, or a portion thereof is subjected to isotope array to determine the level of a second unique marker (FIG. 1, 1004 ; FIG. 2, 2004 ). Isotope arrays allow for functional and phylogenetic screening of active microbial communities in a high-throughput fashion. The technique uses a combination of SIP for monitoring the substrate uptake profiles and microarray technology for determining the taxonomic identities of active microbial communities. Samples are incubated with a ¹⁴C-labeled substrate, which during the course of growth becomes incorporated into microbial biomass. The ¹⁴C-labeled rRNA is separated from unlabeled rRNA and then labeled with fluorochromes. Fluorescent labeled rRNA is hybridized to a phylogenetic microarray followed by scanning for radioactive and fluorescent signals. The technique thus allows simultaneous study of microbial community composition and specific substrate consumption by metabolically active microorganisms of complex microbial communities.

In one embodiment, the sample, or a portion thereof is subjected to a metabolomics assay to determine the level of a second unique marker (FIG. 1, 1004 ; FIG. 2, 2004 ). Metabolomics studies the metabolome which represents the collection of all metabolites, the end products of cellular processes, in a biological cell, tissue, organ or organism. This methodology can be used to monitor the presence of microorganisms and/or microbial mediated processes since it allows associating specific metabolite profiles with different microorganisms. Profiles of intracellular and extracellular metabolites associated with microbial activity can be obtained using techniques such as gas chromatography-mass spectrometry (GC-MS). The complex mixture of a metabolomic sample can be separated by such techniques as gas chromatography, high performance liquid chromatography and capillary electrophoresis. Detection of metabolites can be by mass spectrometry, nuclear magnetic resonance (NMR) spectroscopy, ion-mobility spectrometry, electrochemical detection (coupled to HPLC) and radiolabel (when combined with thin-layer chromatography).

According to the embodiments described herein, the presence and respective number of one or more active microorganism strains in a sample are determined (FIG. 1, 1006 ; FIG. 2, 2006 ). For example, strain identity information obtained from assaying the number and presence of first markers is analyzed to determine how many occurrences of a unique first marker are present, thereby representing a unique microorganism strain (e.g., by counting the number of sequence reads in a sequencing assay). This value can be represented in one embodiment as a percentage of total sequence reads of the first maker to give a percentage of unique microorganism strains of a particular microorganism type. In a further embodiment, this percentage is multiplied by the number of microorganism types (obtained at step 1002 or 2002, see FIG. 1 and FIG. 2 ) to give the absolute abundance of the one or more microorganism strains in a sample and a given volume.

The one or more microorganism strains are considered active, as described above, if the level of second unique marker expression at a threshold level, higher than a threshold value, e.g., higher than at least about 5%, at least about 10%, at least about 20% or at least about 30% over a control level.

In another aspect of the invention, a method for determining the absolute abundance of one or more microorganism strains is determined in a plurality of samples (FIG. 2 , see in particular, 2007). For a microorganism strain to be classified as active, it need only be active in one of the samples. The samples can be taken over multiple time points from the same source, or can be from different environmental sources (e.g., different animals).

The absolute abundance values over samples are used in one embodiment to relate the one or more active microorganism strains, with an environmental parameter (FIG. 2, 2008 ). In one embodiment, the environmental parameter is the presence of a second active microorganism strain. Relating the one or more active microorganism strains to the environmental parameter, in one embodiment, is carried out by determining the co-occurrence of the strain and parameter by correlation or by network analysis.

In one embodiment, determining the co-occurrence of one or more active microorganism strains with an environmental parameter comprises a network and/or cluster analysis method to measure connectivity of strains or a strain with an environmental parameter within a network, wherein the network is a collection of two or more samples that share a common or similar environmental parameter. In another embodiment, the network and/or cluster analysis method may be applied to determining the co-occurrence of two or more active microorganism strains in a sample (FIG. 2, 2008 ). In another embodiment, the network analysis comprises nonparametric approaches including mutual information to establish connectivity between variables. In another embodiment, the network analysis comprises linkage analysis, modularity analysis, robustness measures, betweenness measures, connectivity measures, transitivity measures, centrality measures or a combination thereof (FIG. 2, 2009 ). In another embodiment, the cluster analysis method comprises building a connectivity model, subspace model, distribution model, density model, or a centroid model and/or using community detection algorithms such as the Louvain, Bron-Kerbosch, Girvan-Newman, Clauset-Newman-Moore, Pons-Latapy, and Wakita-Tsurumi algorithms (FIG. 2, 2010 ).

In one embodiment, the cluster analysis method is a heuristic method based on modularity optimization. In a further embodiment, the cluster analysis method is the Louvain method. See, e.g., the method described by Blondel et al. (2008). Fast unfolding of communities in large networks. Journal of Statistical Mechanics: Theory and Experiment, Volume 2008, October 2008, incorporated by reference herein in its entirety for all purposes.

In another embodiment, the network analysis comprises predictive modeling of network through link mining and prediction, collective classification, link-based clustering, relational similarity, or a combination thereof. In another embodiment, the network analysis comprises differential equation based modeling of populations. In another embodiment, the network analysis comprises Lotka-Volterra modeling.

In one embodiment, relating the one or more active microorganism strains to an environmental parameter (e.g., determining the co-occurrence) in the sample comprises creating matrices populated with linkages denoting environmental parameter and microorganism strain associations.

In one embodiment, the multiple sample data obtained at step 2007 (e.g., over two or more samples which can be collected at two or more time points where each time point corresponds to an individual sample), is compiled. In a further embodiment, the number of cells of each of the one or more microorganism strains in each sample is stored in an association matrix (which can be in some embodiments, an abundance matrix). In one embodiment, the association matrix is used to identify associations between active microorganism strains in a specific time point sample using rule mining approaches weighted with association (e.g., abundance) data. Filters are applied in one embodiment to remove insignificant rules.

In one embodiment, the absolute abundance of one or more, or two or more active microorganism strains is related to one or more environmental parameters (FIG. 2, 2008 ), e.g., via co-occurrence determination. Environmental parameters are chosen by the user depending on the sample(s) to be analyzed and are not restricted by the methods described herein. The environmental parameter can be a parameter of the sample itself, e.g., pH, temperature, amount of protein in the sample. Alternatively, the environmental parameter is a parameter that affects a change in the identity of a microbial community (i.e., where the “identity” of a microbial community is characterized by the type of microorganism strains and/or number of particular microorganism strains in a community), or is affected by a change in the identity of a microbial community. For example, an environmental parameter in one embodiment, is the food intake of an animal or the amount of eggs produced by poultry. In one embodiment, the environmental parameter is the presence, activity and/or abundance of a second microorganism strain in the microbial community, present in the same sample.

In some embodiments described herein, an environmental parameter is referred to as a metadata parameter.

Other examples of metadata parameters include but are not limited to genetic information from the host from which the sample was obtained (e.g., DNA mutation information), sample pH, sample temperature, expression of a particular protein or mRNA, nutrient conditions (e.g., level and/or identity of one or more nutrients) of the surrounding environment/ecosystem), susceptibility or resistance to disease, onset or progression of disease, susceptibility or resistance of the sample to toxins, efficacy of xenobiotic compounds (pharmaceutical drugs), biosynthesis of natural products, or a combination thereof.

For example, according to one embodiment, microorganism strain number changes are calculated over multiple samples according to the method of FIG. 2 (i.e., at 2001-2007). Strain number changes of one or more active strains over time is compiled (e.g., one or more strains that have initially been identified as active according to step 2006), and the directionality of change is noted (i.e., negative values denoting decreases, positive values denoting increases). The number of cells over time is represented as a network, with microorganism strains representing nodes and the abundance weighted rules representing edges. Markov chains and random walks are leveraged to determine connectivity between nodes and to define clusters. Clusters in one embodiment are filtered using metadata in order to identify clusters associated with desirable metadata (FIG. 2, 2008 ).

In a further embodiment, microorganism strains are ranked according to importance by integrating cell number changes over time and strains present in target clusters, with the highest changes in cell number ranking the highest.

Network and/or cluster analysis method in one embodiment, is used to measure connectivity of the one or more strains within a network, wherein the network is a collection of two or more samples that share a common or similar environmental parameter. In one embodiment, network analysis comprises linkage analysis, modularity analysis, robustness measures, betweenness measures, connectivity measures, transitivity measures, centrality measures or a combination thereof. In another embodiment, network analysis comprises predictive modeling of network through link mining and prediction, social network theory, collective classification, link-based clustering, relational similarity, or a combination thereof. In another embodiment, network analysis comprises differential equation based modeling of populations. In yet another embodiment, network analysis comprises Lotka-Volterra modeling.

Cluster analysis method comprises building a connectivity model, subspace model, distribution model, density model, or a centroid model.

Network and cluster based analysis, for example, to carry out method step 2008 of FIG. 2 , can be carried out via a module. As used herein, a module can be, for example, any assembly, instructions and/or set of operatively-coupled electrical components, and can include, for example, a memory, a processor, electrical traces, optical connectors, software (executing in hardware) and/or the like.

Network Analysis

A network and/or cluster analysis method, in one embodiment, is used to measure connectivity of the one or more strains within a network, wherein the network is a collection of two or more samples that share a common or similar environmental parameter. In one embodiment, network analysis comprises linkage analysis, modularity analysis, robustness measures, betweenness measures, connectivity measures, transitivity measures, centrality measures or a combination thereof. In another embodiment, network analysis comprises predictive modeling of network through link mining and prediction, social network theory, collective classification, link-based clustering, relational similarity, or a combination thereof. In another embodiment, network analysis comprises mutual information, maximal information coefficient (MIC) calculations, or other nonparametric methods between variables to establish connectivity. In another embodiment, network analysis comprises differential equation based modeling of populations. In yet another embodiment, network analysis comprises Lotka-Volterra modeling.

The environmental parameter can be a parameter of the sample itself, e.g., pH, temperature, amount of protein in the sample. Alternatively, the environmental parameter is a parameter that affects a change in the identity of a microbial community (i.e., where the “identity” of a microbial community is characterized by the type of microorganism strains and/or number of particular microorganism strains in a community), or is affected by a change in the identity of a microbial community. For example, an environmental parameter in one embodiment, is the food intake of an animal or the amount of eggs produced. In one embodiment, the environmental parameter is the presence, activity and/or abundance of a second microorganism strain in the microbial community, present in the same sample. In some embodiments, an environmental parameter is referred to as a metadata parameter.

Other examples of metadata parameters include but are not limited to genetic information from the host from which the sample was obtained (e.g., DNA mutation information), sample pH, sample temperature, expression of a particular protein or mRNA, nutrient conditions (e.g., level and/or identity of one or more nutrients) of the surrounding environment/ecosystem), susceptibility or resistance to disease, onset or progression of disease, susceptibility or resistance of the sample to toxins, efficacy of xenobiotic compounds (pharmaceutical drugs), biosynthesis of natural products, or a combination thereof.

Poultry Pathogen Resistance and Clearance

In some aspects, the present disclosure is drawn to administering one or more microbial compositions described herein to poultry to clear the gastrointestinal tract of pathogenic microbes. In some embodiments, the present disclosure is further drawn to administering microbial compositions described herein to prevent colonization of pathogenic microbes in the gastrointestinal tract. In some embodiments, the administration of microbial compositions described herein further clear pathogens from the integument and the respiratory tract of poultry, and/or prevent colonization of pathogens on the integument and in the respiratory tract. In some embodiments, the administration of microbial compositions described herein reduce leaky gut/intestinal permeability, inflammation, and/or incidence of liver disease. In some embodiments, the administration of microbial compositions described herein promote the development of the immune system.

In some embodiments, the microbial compositions of the present disclosure comprise one or more microbes that are present in the gastrointestinal tract of poultry at a relative abundance of less than 15%, 14%, 13%, 12%, 11%, 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, 0.5%, 0.1%, or 0.01%.

In some embodiments, after administration of microbial compositions of the present disclosure the one or more microbes are present in the gastrointestinal tract of the poultry at a relative abundance of at least 0.5%, 1%, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, or 95%.

Pathogenic microbes of poultry include the following: Mycoplasma gallisepticum, Mycoplasma meleagridis, Mycoplasma synoviae, Pasteurella multocida, Clostridium perfringens, Clostridium colinum, Clostridium botulinum, Salmonella typi, Salmonella typhimurium, Salmonella enterica, Salmonella pullorum, Salmonella gallinarum, Hemophilus gallinarum, Erysipelothrix insidiosa, Campylobacter jejuni, Campylobacter coli, Campylobacter lari, Listeria monocytogenes, Arcobacter butzleri, Mycobacterium avium, and pathogenic strains of Escherichia coli and Staphylococcus aureus. In some embodiments, the pathogenic microbes include viral pathogens. In some embodiments, the pathogenic microbes are pathogenic to both poultry and humans. In some embodiments, the pathogenic microbes are pathogenic to either poultry or humans.

In some embodiments, the administration of compositions of the present disclosure to poultry modulate the makeup of the gastrointestinal microbiome such that the administered microbes outcompete microbial pathogens present in the gastrointestinal tract. In some embodiments, the administration of compositions of the present disclosure to poultry harboring microbial pathogens outcompetes the pathogens and clears the poultry of the pathogens. In some embodiments, the administration of compositions of the present disclosure stimulate host immunity, and aids in clearance of the microbial pathogens. In some embodiments, the administration of compositions of the present disclosure introduce microbes that produce bacteriostatic and/or bactericidal components that decrease or clear the poultry of the microbial pathogens. In some embodiments, the administration of compositions of the present disclosure introduces microbes that modulate the pH, nutrient availability, minteral compostions, and/or vitamin composition of the gastrointestinal tract. In some embodiments, the administration of compositons of the present disclosure introduces microbes that increase the gastrointestinal pH, resulting in the inhibition of pathogen growth. In some embodiments, the administration of compositons of the present disclosure introduces microbes that decrease the gastrointestinal pH, resulting in the inhibition of pathogen growth.

In some embodiments, challenging poultry with a microbial colonizer or microbial pathogen after administering one or more compositions of the present disclosure prevents the microbial colonizer or microbial pathogen from growing to a relative abundance of greater than 15%, 4%1, 3%1, 12%, 11%, 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%1, %, 0.5%, 0.1%, or 0.01%. In further embodiments, challenging poultry with a microbial colonizer or microbial pathogen after administering one or more compositions of the present disclosure prevents the microbial colonizer or microbial pathogen from colonizing poultry

In some embodiments, clearance of the microbial colonizer or microbial pathogen occurs occurs in less than 25 days, less than 24 days, less than 23 days, less than 22 days, less than 21 days, less than 20 days, less than 19 days, less than 18 days, less than 17 days, less than 16 days, less than 15 days, less than 14 days, less than 13 days, less than 12 days, less than 11 days, less than 10 days, less than 9 days, less than 8 days, less than 7 days, less than 6 days, less than 5 days, less than 4 days, less than 3 days, or less than 2 days post administration of the one or more compositions of the present disclosure.

In some embodiments, clearance of the microbial colonizer or microbial pathogen occurs within 1-30 days, 1-25 days, 1-20 day, 1-15 days, 1-10 days, 1-5 days, 5-30 days, 5-25 days, 5-20 days, 5-15 days, 5-10 days, 10-30 days, 10-25 days, 10-20 days, 10-15 days, 15-30 days, 15-25 days, 15-20 days, 20-30 days, 20-25 days, or 25-30 days post administration of the one or more compositions of the present disclosure.

Improved Traits

In some aspects, the present disclosure is drawn to administering microbial compositions described herein to poultry to improve one or more desirable traits such as the modulation of aspects of weight, musculature, meat characteristics, egg quantity, egg weight, egg volume, egg quality, egg shell density, digestive chemistry, efficiency of feed utilization and digestibility, fecal output, methane production, overall bird health, prevention of colonization of pathogenic microbes, and clearance of pathogenic microbes. In some aspects, the improvement of traits includes an improvement of the innate immune response in poultry or eggs of poultry. In some aspects, the improved innate immune response is an increase or decrease of lysozyme, steroids, avidin, apoprotein, ovomucoid, ovomucin, ovoflavoprotein, ovoinhibitor, or conalbumin in the poultry or eggs of poultry. In some aspects, the improvement of traits include an increased success in hatching, an increased incidence of normal chick morphology, and increased incidence of embryo survival, an increased growth rate in chicks and or embryos, an increase in total body mass in chicks and poultry, and and increase or decrease in egg-white proteins.

In some aspects, the improvement of one or more desirable traits is an improvement of 2, 3, 4, 5, 6, 7, 8, 9, or 10 desirable traits in poultry by the administration of microbial compositions described herein.

In some embodiments, the increase in egg quantity is an increase of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 eggs relative to an animal not having been administered a composition of the present disclosure. In some embodiments, the increase in egg quantity is an increase of less than 2, 3, 4, 5, 6, 7, 8, 9, or 10 eggs relative to an animal not having been administered a composition of the present disclosure. In some embodiments, the increase in egg quantity is an increase of at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 110%, 120%, 130%, 140%, 150%, 160%, 170%, 180%, 190%, or 200% relative to an animal not having been administered a composition of the present disclosure.

In some embodiments, the increase in egg volume is an increase of at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% relative to an animal not having been administered a composition of the present disclosure. In some embodiments, the increase in egg volume is an increase of less than 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% relative to an animal not having been administered a composition of the present disclosure.

In some embodiments, the fecal output is reduced by at least 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% relative to an animal not having been administered a composition of the present disclosure. In some embodiments, the fecal output is reduced by less than 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% relative to an animal not having been administered a composition of the present disclosure.

In some embodiments, the poultry having been administered a composition of the present disclosure exhibit a weight gain of at least 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% relative to a poultry not having been administered a composition of the present disclosure.

In some embodiments, the poultry having been administered a composition of the present disclosure exhibit a weight gain of at least about 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% relative to a poultry not having been administered a composition of the present disclosure.

In some embodiments, the poultry having been administered a composition of the present disclosure exhibit a feed conversion ratio decrease of at least 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9% 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% relative to a poultry not having been administered a composition of the present disclosure.

In some embodiments, the poultry having been administered a composition of the present disclosure exhibit a feed conversion ratio decrease of at least about 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% relative to a poultry not having been administered a composition of the present disclosure.

In some embodiments, the poultry having been administered a composition of the present disclosure exhibit a decrease in the number of necrotic enteritis-causing bacteria in the gastrointestinal tract of at least 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% relative to a poultry not having been administered a composition of the present disclosure.

In some embodiments, the poultry having been administered a composition of the present disclosure exhibit a decrease in the number of necrotic enteritis-causing bacteria in the gastrointestinal tract of at least about 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% relative to a poultry not having been administered a composition of the present disclosure.

In some embodiments, the poultry having been administered a composition of the present disclosure exhibit a decrease in the number of pathogenic bacteria in the gastrointestinal tract of at least 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% relative to a poultry not having been administered a composition of the present disclosure.

In some embodiments, the poultry having been administered a composition of the present disclosure exhibit a decrease in the number of human pathogenic bacteria in the gastrointestinal tract of at least about 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9% 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% relative to a poultry not having been administered a composition of the present disclosure.

In some embodiments, the poultry having been administered a composition of the present disclosure exhibit a decrease in the number of poultry pathogenic bacteria in the gastrointestinal tract of at least about 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9% 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% relative to poultry not having been administered a composition of the present disclosure.

In some embodiments, the weight of a flock or flocks of poultry having been administered a composition of the present disclosure exhibit a decrease in the coefficient of variation of at least about 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% relative to a flock of poultry not having been administered a composition of the present disclosure.

In some embodiments, the weight of a flock or flocks of poultry having been administered a composition of the present disclosure exhibit an increase in flock uniformity of at least about 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% relative to a flock of poultry not having been administered a composition of the present disclosure.

In some embodiments, the mortality of a flock or flocks of poultry having been administered a composition of the present disclosure exhibit a decrease in mortality of at least about 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% relative to a flock of poultry not having been administered a composition of the present disclosure.

In some embodiments, improving the eggs produced by poultry is desirable, wherein the eggs include triglycerides, triacylglycerides, diacylglycerides, monoacylglycerides, phospholipids, cholesterol, glycolipids, and free fatty acids. In further embodiments, free fatty acids include short chain fatty acids (i.e., C4:0, C6:0, and C8:0), medium chain fatty acids (i.e., C10:0, C10:1, C12:0, C14:0, C14:1, and C15:0), and long chain fatty acids (i.e., C16:0, C16:1, C17:0, C17:1, C18:0, C18:1, C18:2, C18:3, and C20:0).

In some embodiments, improving the quantity or concentration of vitamins in eggs produced by poultry is desirable. Vitamins found in eggs include B1, B2, B3, B5, B6, B12, choline, biotin, and folic acid.

In some embodiments, improving the quantity or concentration of minerals in eggs produced by poultry is desirable. Minerals found in eggs include phosphorous, iodine, selenium, and calcium. Trace amounts of the following may be found in eggs: barium, copper, iron, manganese, nickel, lead, selenium, strontium, vanadium, selenium, rubidium, and zinc.

In some embodiments, increasing or decreasing chicken serum levels of calcium, phosphorous, magnesium, triglycerides, cholesterol, and saccharides is desirable. The modulation of these serum components impact egg traits such as thickness, porosity, density, nutritional content, desirable taste, fat content, cholesterol content, and coloration.

In some embodiments, improving the efficiency and digestibility of animal feed is desirable. In some embodiments, increasing the degradation of lignocellulosic components from animal feed is desirable. Lignocellulosic components include lignin, cellulose, and hemicellulose.

In some embodiments, increasing the concentration of fatty acids in the gastrointestinal tract is desirable. Fatty acids include acetic acid, propionic acid, and butyric acid. In some embodiments, maintaining the pH balance in the gastrointestinal tract to prevent destruction of beneficial microbial bioensembles is desirable. In some embodiments, increasing the concentration of lactic acids in the gastrointestinal tract is desirable. Lactic acid is lowers the pH of the surrounding environment, including intracellular pH which can disrupt microbial proton motive force. Lactic acid can also permeabilized the outer membrane of gram-negative bacteria such that they exhibit an increased susceptibility to antimicrobials.

In some embodiments, decreasing the amount of methane and manure produced by poultry is desirable

In some embodiments, a decrease in the amount of total manure produced is desirable. In further embodiments, a decrease in the total amount of phosphorous and/or nitrogen in the total manure produced is desirable.

In some embodiments, improving the feed intake is desirable. In some embodiments, improving the efficiency of nitrogen utilization of the feed and/or dry matter ingested by poultry is desirable.

In some embodiments, the improved traits of the present disclosure are the result of the administration of the presently described microbial compositions. It is thought that the microbial compositions modulate the microbiome of poultry such that the biochemistry of one or more elements of the gastrointestinal tract is changed in such a way that the gastrointestinal liquid and solid substratum are more efficiently and more completely degraded into subcomponents and metabolites than the gastrointestinal tract of poultry not having been administered microbial compositions of the present disclosure.

In some embodiments, the increase in efficiency and the increase of degradation of the gastrointestinal substratum result in an increase in improved traits of the present disclosure.

In some embodiments, the improvement of any one or more of the traits of the present disclosure is a change of about 0.1%, about 0.2%, about 0.3%, about 0.4%, about 0.5%, about 0.6%, about 0.7%, about 0.8%, about 0.9%, about 1%, about 2%, about 3%, about 4%, about 5%, about 6%, about 7%, about 8%, about 9%, about 10%, about 11%, about 12%, about 13%, about 14%, about 15%, about 16%, about 17%, about 18%, about 19%, about 20%, about 21%, about 22%, about 23%, about 24%, about 25%, about 26%, about 27%, about 28%, about 29%, about 30%, about 31%, about 32%, about 33%, about 34%, about 35%, about 36%, about 37%, about 38%, about 39%, about 40%, about 41%, about 42%, about 43%, about 44%, about 45%, about 46%, about 47%, about 48%, about 49%, about 50%, about 51%, about 52%, about 53%, about 54%, about 55%, about 56%, about 57%, about 58%, about 59%, about 60%, about 61%, about 62%, about 63%, about 64%, about 65%, about 66%, about 67%, about 68%, about 69%, about 70%, about 71%, about 72%, about 73%, about 74%, about 75%, about 76%, about 77%, about 78%, about 79%, about 80%, about 81%, about 82%, about 83%, about 84%, about 85%, about 86%, about 87%, about 88%, about 89%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or about 100% relative to the animal not having been administered one or more microbial compositions of the present disclosure.

In some embodiments, the improvement of any one or more of the traits of the present disclosure is a change of at least 0.1%, at least 0.2%, at least 0.3%, at least 0.4%, at least 0.5%, at least 0.6%, at least 0.7%, at least 0.8%, at least 0.9%, at least 1%, at least 2%, at least 3%, at least 4%, at least 5%, at least 6%, at least 7%, at least 8%, at least 9%, at least 10%, at least 11%, at least 12%, at least 13%, at least 14%, at least 15%, at least 16%, at least 17%, at least 18%, at least 19%, at least 20%, at least 21%, at least 22%, at least 23%, at least 24%, at least 25%, at least 26%, at least 27%, at least 28%, at least 29%, at least 30%, at least 31%, at least 32%, at least 33%, at least 34%, at least 35%, at least 36%, at least 37%, at least 38%, at least 39%, at least 40%, at least 41%, at least 42%, at least 43%, at least 44%, at least 45%, at least 46%, at least 47%, at least 48%, at least 49%, at least 50%, at least 51%, at least 52%, at least 53%, at least 54%, at least 55%, at least 56%, at least 57%, at least 58%, at least 59%, at least 60%, at least 61%, at least 62%, at least 63%, at least 64%, at least 65%, at least 66%, at least 67%, at least 68%, at least 69%, at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 100% relative to the animal not having been administered one or more microbial compositions of the present disclosure.

In some embodiments, the increase of any one or more of the traits of the present disclosure is an increase of about 0.1%, about 0.2%, about 0.3%, about 0.4%, about 0.5%, about 0.6%, about 0.7%, about 0.8%, about 0.9%, about 1%, about 2%, about 3%, about 4%, about 5%, about 6%, about 7%, about 8%, about 9%, about 10%, about 11%, about 12%, about 13%, about 14%, about 15%, about 16%, about 17%, about 18%, about 19%, about 20%, about 21%, about 22%, about 23%, about 24%, about 25%, about 26%, about 27%, about 28%, about 29%, about 30%, about 31%, about 32%, about 33%, about 34%, about 35%, about 36%, about 37%, about 38%, about 39%, about 40%, about 41%, about 42%, about 43%, about 44%, about 45%, about 46%, about 47%, about 48%, about 49%, about 50%, about 51%, about 52%, about 53%, about 54%, about 55%, about 56%, about 57%, about 58%, about 59%, about 60%, about 61%, about 62%, about 63%, about 64%, about 65%, about 66%, about 67%, about 68%, about 69%, about 70%, about 71%, about 72%, about 73%, about 74%, about 75%, about 76%, about 77%, about 78%, about 79%, about 80%, about 81%, about 82%, about 83%, about 84%, about 85%, about 86%, about 87%, about 88%, about 89%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or about 100% relative to the animal not having been administered one or more microbial compositions of the present disclosure.

In some embodiments, the increase of any one or more of the traits of the present disclosure is an increase of at least 0.1%, at least 0.2%, at least 0.3%, at least 0.4%, at least 0.5%, at least 0.6%, at least 0.7%, at least 0.8%, at least 0.9%, at least 1%, at least 2%, at least 3%, at least 4%, at least 5%, at least 6%, at least 7%, at least 8%, at least 9%, at least 10%, at least 11%, at least 12%, at least 13%, at least 14%, at least 15%, at least 16%, at least 17%, at least 18%, at least 19%, at least 20%, at least 21%, at least 22%, at least 23%, at least 24%, at least 25%, at least 26%, at least 27%, at least 28%, at least 29%, at least 30%, at least 31%, at least 32%, at least 33%, at least 34%, at least 35%, at least 36%, at least 37%, at least 38%, at least 39%, at least 40%, at least 41%, at least 42%, at least 43%, at least 44%, at least 45%, at least 46%, at least 47%, at least 48%, at least 49%, at least 50%, at least 51%, at least 52%, at least 53%, at least 54%, at least 55%, at least 56%, at least 57%, at least 58%, at least 59%, at least 60%, at least 61%, at least 62%, at least 63%, at least 64%, at least 65%, at least 66%, at least 67%, at least 68%, at least 69%, at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 100% relative to the animal not having been administered one or more microbial compositions of the present disclosure.

In some embodiments, the decrease of any one or more of the traits of the present disclosure is a decrease of about 0.1%, about 0.2%, about 0.3%, about 0.4%, about 0.5%, about 0.6%, about 0.7%, about 0.8%, about 0.9%, about 1%, about 2%, about 3%, about 4%, about 5%, about 6%, about 7%, about 8%, about 9%, about 10%, about 11%, about 12%, about 13%, about 14%, about 15%, about 16%, about 17%, about 18%, about 19%, about 20%, about 21%, about 22%, about 23%, about 24%, about 25%, about 26%, about 27%, about 28%, about 29%, about 30%, about 31%, about 32%, about 33%, about 34%, about 35%, about 36%, about 37%, about 38%, about 39%, about 40%, about 41%, about 42%, about 43%, about 44%, about 45%, about 46%, about 47%, about 48%, about 49%, about 50%, about 51%, about 52%, about 53%, about 54%, about 55%, about 56%, about 57%, about 58%, about 59%, about 60%, about 61%, about 62%, about 63%, about 64%, about 65%, about 66%, about 67%, about 68%, about 69%, about 70%, about 71%, about 72%, about 73%, about 74%, about 75%, about 76%, about 77%, about 78%, about 79%, about 80%, about 81%, about 82%, about 83%, about 84%, about 85%, about 86%, about 87%, about 88%, about 89%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or about 100% relative to the animal not having been administered one or more microbial compositions of the present disclosure.

In some embodiments, the decrease of any one or more of the traits of the present disclosure is a decrease of at least 0.1%, at least 0.2%, at least 0.3%, at least 0.4%, at least 0.5%, at least 0.6%, at least 0.7%, at least 0.8%, at least 0.9%, at least 1%, at least 2%, at least 3%, at least 4%, at least 5%, at least 6%, at least 7%, at least 8%, at least 9%, at least 10%, at least 11%, at least 12%, at least 13%, at least 14%, at least 15%, at least 16%, at least 17%, at least 18%, at least 19%, at least 20%, at least 21%, at least 22%, at least 23%, at least 24%, at least 25%, at least 26%, at least 27%, at least 28%, at least 29%, at least 30%, at least 31%, at least 32%, at least 33%, at least 34%, at least 35%, at least 36%, at least 37%, at least 38%, at least 39%, at least 40%, at least 41%, at least 42%, at least 43%, at least 44%, at least 45%, at least 46%, at least 47%, at least 48%, at least 49%, at least 50%, at least 51%, at least 52%, at least 53%, at least 54%, at least 55%, at least 56%, at least 57%, at least 58%, at least 59%, at least 60%, at least 61%, at least 62%, at least 63%, at least 64%, at least 65%, at least 66%, at least 67%, at least 68%, at least 69%, at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 100% relative to the animal not having been administered one or more microbial compositions of the present disclosure.

In some embodiments, the villi of the gastrointestinal tract of poultry increase in diameter and/or length upon administration of one or more microbes and/or bioensembles of the present disclosure.

In some embodiments, the villi of the gastrointestinal track of poultry increase in diameter and/or length upon administration of one or more microbes and/or bioensembles of the present disclosure by at least 1 μM, at least 2 μM, at least 3 μM, at least 4 μM, at least 5 μM, at least 6 M, at least 7 μM, at least 8 μM, at least 9 μM, at least 10 μM, at least 11 μM, at least 12 μM, at least 13 μM, at least 14 μM, at least 15 μM, at least 16 μM, at least 17 μM, at least 18 μM, at least 18 μM, at least 20 μM, at least 21 μM, at least 22 μM, at least 23 μM, at least 24 μM, at least 25 M, at least 30 μM, at least 35 μM, at least 40 μM, at least 45 μM, at least 50 μM, at least 55 μM, at least 60 μM, at least 65 μM, at least 70 μM, at least 75 μM, at least 80 μM, at least 85 μM, at least 90 μM, at least 95 μM, at least 100 μM, at least 110 μM, at least 120 μM, at least 130 μM, at least 140 μM, at least 150 μM, at least 160 μM, at least 170 μM, at least 180 μM, at least 190 M, or at least 200 μM.

In some embodiments, the villi of the gastrointestinal track of poultry increase in diameter and/or length upon administration of one or more microbes and/or bioensembles of the present disclosure by less than 1 μM, less than 2 μM, less than 3 μM, less than 4 μM, less than 5 μM, less than 6 μM, less than 7 μM, less than 8 μM, less than 9 μM, less than 10 μM, less than 11 μM, less than 12 μM, less than 13 μM, less than 14 μM, less than 15 μM, less than 16 μM, less than 17 μM, less than 18 μM, less than 18 μM, less than 20 μM, less than 21 μM, less than 22 μM, less than 23 M, less than 24 μM, less than 25 μM, less than 30 μM, less than 35 μM, less than 40 μM, less than 45 μM, less than 50 μM, less than 55 μM, less than 60 μm, less than 65 μM, less than 70 μM, less than 75 μM, less than 80 μM, less than 85 μM, less than 90 μM, less than 95 μM, less than 100 μM, less than 110 μM, less than 120 μM, less than 130 μM, less than 140 μM, less than 150 M, less than 160 μM, less than 170 μM, less than 180 μM, less than 190 μM, or less than 200 M.

In some embodiments, the ileum or ileal tissue of poultry is thinner upon administration of one or more microbes and/or bioensembles of the present disclosure. The ileal tissue is defined as the tissue of the ileam that spans the lumen to the basal membrane.

In some embodiments, the ileum or ileal tissue of poultry is thinner upon administration of one or more microbes and/or bioensembles of the present disclosure by at least 1 μM, at least 2 M, at least 3 μM, at least 4 μM, at least 5 μM, at least 6 μM, at least 7 μM, at least 8 μM, at least 9 μM, at least 10 μM, at least 11 μM, at least 12 μM, at least 13 μM, at least 14 μM, at least 15 M, at least 16 μM, at least 17 μM, at least 18 μM, at least 18 μM, at least 20 μM, at least 21 μM, at least 22 μM, at least 23 μM, at least 24 μM, at least 25 μM, at least 30 μM, at least 35 μM, at least 40 μM, at least 45 μM, at least 50 μM, at least 55 μM, at least 60 μM, at least 65 μM, at least 70 μM, at least 75 μM, at least 80 μM, at least 85 μM, at least 90 μM, at least 95 μM, at least 100 M, at least 110 μM, at least 120 μM, at least 130 μM, at least 140 μM, at least 150 μM, at least 160 μM, at least 170 μM, at least 180 μM, at least 190 μM, or at least 200 μM.

In some embodiments, the ileum or ileal tissue of poultry is thinner upon administration of one or more microbes and/or bioensembles of the present disclosure by less than 1 μM, less than 2 μM, less than 3 μM, less than 4 μM, less than 5 μM, less than 6 μM, less than 7 μM, less than 8 M, less than 9 μM, less than 10 μM, less than 11 μM, less than 12 μM, less than 13 μM, less than 14 μM, less than 15 μM, less than 16 μM, less than 17 μM, less than 18 μM, less than 18 μM, less than 20 μM, less than 21 μM, less than 22 μM, less than 23 μm, less than 24 μM, less than 25 μM, less than 30 μM, less than 35 μM, less than 40 μM, less than 45 μM, less than 50 μM, less than 55 M, less than 60 μM, less than 65 μM, less than 70 μM, less than 75 μM, less than 80 μM, less than 85 μM, less than 90 μM, less than 95 μM, less than 100 μM, less than 110 μM, less than 120 M, less than 130 μM, less than 140 μM, less than 150 μM, less than 160 μM, less than 170 μM, less than 180 μM, less than 190 μM, or less than 200 μM.

In some embodiments, the digestibility of fats is increased or improved in poultry upon the administration of one or more microbes and/or bioensembles of the present disclosure. In some embodiments, a measurement of crude fat utilized is determined by subtracting the fat in the excreta from the fat in the food eaten.

In some embodiments, the digestibility of fats is increased or improved in poultry upon the administration of one or more microbes and/or bioensembles of the present disclosure by at least 0.5%, at least 1%, at least 5%, at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95%. In some embodiments, the digestibility of fats is measured by the crude fat in the excreta subtracted from the crude fat in the food eaten. See Duerr et al. (2017. J. Avian Med. Surg. 31(2):132-141.)

In some embodiments, the digestibility of amino acids or oligo-/polypeptides is increased or improved in poultry upon the administration of one or more microbes and/or bioensembles of the present disclosure.

In some embodiments, the digestibility of amino acids or oligo-/polypeptides is increased or improved in poultry upon the administration of one or more microbes and/or bioensembles of the present disclosure by at least 0.5%, at least 1%, at least 5%, at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95%.

In some embodiments, the digestibility of retinol and/or lutein is increased or improved in poultry upon the administration of one or more microbes and/or bioensembles of the present disclosure.

In some embodiments, the digestibility of retinol and/or lutein is increased or improved in poultry upon the administration of one or more microbes and/or bioensembles of the present disclosure by at least 0.5%, at least 1%, at least 5%, at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95%.

In some embodiments, the absorption of calcium, iron, zinc, copper, phosphorous, or ions thereof, is increased or improved in poultry upon the administration of one or more microbes and/or bioensembes of the present disclosure.

In some embodiments, the absorption of calcium, iron, zinc, copper, phosphorous, or ions thereof, is increased or improved in poultry upon the administration of one or more microbes and/or bioensembes of the present disclosure by at least 0.5%, at least 1%, at least 5%, at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95%.

In some embodiments, the occurrence of foamy digests in the gastrointestinal tract in poultry upon the administration of one or more microbes and/or bioensembles of the present disclosure.

In some embodiments, the occurrence of foamy digests in the gastrointestinal tract in poultry upon the administration of one or more microbes and/or bioensembles of the present disclosure by at least 0.5%, at least 1%, at least 5%, at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95%.

In some embodiments, the production of methane in the gastrointestinal tract in poultry is decreased upon the administration of one or more microbes and/or bioensembles of the present disclosure.

In some embodiments, the production of methane in the gastrointestinal tract in poultry is decreased upon the administration of one or more microbes and/or bioensembles of the present disclosure by at least 0.5%, at least 1%, at least 5%, at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95%.

Mode of Action: Gastrointestinal Health Improvement and Competitive Exclusion

The influence of the gastrointestinal microbiome on broiler health is well known (Roberts, 2015; Yeoman, 2012; Lee (presentation); Oakley, 2014)—a healthy intestinal system will improve the overall welfare and performance of birds in a commercial farm setting. Although the exact roles and mechanisms of individual species within this intricate and complicated system are still largely unknown, the overall beneficial effects of microorganisms on the host's health and performance have been studied. The current knowledge of metabolism and mechanisms of action are summarized below. See FIG. 5 . (Pourabedin and Zhao. 2015. FEMS Microbiol. Lett. 362:fnv122). FIG. 5 depicts a suite of interactions that are all modulated by the composition of the gastrointestinal tract with a well-balanced population of commensal microbes with an adequate supply of prebiotic compositions. For example, the commensal bacteria are (1) producing antibacterial compounds to compete with other organisms, including pathogens, (2) producing simple fatty acids involved in metabolic regulation and energy use, (3) immunomodulating the localized immune responses in conjunction with lymphocytes and antigen presenting cells, etc.

General Nutrition and Gut Health

Increasing the Concentration of Beneficial Molecules, Including Short Chain Fatty Acids and Other Organic Acids, in the Gastrointestinal Tract of the Broiler Improves Bird Performance.

Microbial short chain fatty acid production, in particular, are absorbed and metabolized by the bird and can provide 5% to 15% of the daily requirements for bird maintenance energy (Chichlowski, 2007; Annison, 1968; Gasaway, 1976ab). Previous studies have shown that supplementation of butyrate can improve both overall weight gain and feed-conversion when administered daily to the bird, and that supplementation of any organic acid (including fumaric and lactic) can improve bird weight gain (Levy, 2015; Gilliland, 1977; Afil, 2010). Levy, et al. (2015) showed that improvements in body weight gain and feed conversion increased linearly with increasing concentrations of encapsulated butyric acid levels. Butyrate also enhances vili development (Chamba, 2014) activates the immune response, and can also have a direct bactericidal effect (Gantois, 2006).

Improving Development of the Gastrointestinal Tract, Enhancing Villi Growth, and Stimulating the Immune System.

Supplementation of butyrate and other organic acids to the diets of birds have been shown to enhance vili development and stimulate the immune system (Chamba, 2014; Adil 2010; Adil 2011).

Improving Apparent Metabolizable Energy of the Diet

Fermentation of various microbes can convert carbohydrates to various end products. Most short chain fatty acids produced by these microorganisms are absorbed and utilized by the bird (Rinttila, 2013; Annison, 1968; Gasaway, 1976ab). The synthesis of vitamins, including vitamins B and K, are also carried out by microorganisms (Cummings, 1997).

Competitive Exclusion

Bacteriocin Production

Microorganisms within the gastrointestinal tract self-regulate through the production of various antimicrobial chemicals. Bacteriocins, for example, are commonly produced by lactic acid microorganisms and can prevent the colonization of pathogens (Chen, 2007; Juven 1990). Short-chain fatty acids been shown to impact and inhibit enteric bacteria including Salmonella typhimurium, but do not inhibit beneficial, native microorganisms (Van der Wielen et al., 2000). Both propionic acid, butyric acid, acetate has also been shown to inhibit pathogenic bacteria (Marounek, 1999; Van der Wielen, 2000; Immerseei, 2003).

Competitive Use of Nutrients/Binding Sites

Birds are first inoculated with microorganisms shortly after birth. As the bird continues to develop, the microbiome colonizes and establishes itself, ultimately creating a stable ecosystems that houses organisms that occupy all niches and utilizes all available nutrients (Callaway, 2008). This expansive, stable community can prevent pathogens from colonizing.

Creating Environments that are not Conducive to Pathogen Growth

Microorganisms residing within the gut reduce the redox potential within the gut, creating an environment suitable for obligate anaerobes to flourish (Cummings, 1997; Chicklowki, 20017; Juven 1990). Lactate and other short chain fatty acid production lowers the pH of the gastrointestinal environment, making it more difficult for pathogens to colonize and grow (Pourabedin, 2015). Native microorganisms have also been shown to neutralize enterotoxins (M'Sadeq, 2015).

EXAMPLES Example I. Administration and Colonization of Native Bacteria Fed to Young Broiler Chicks

Purpose: Determine the colonization efficacy of native microorganisms fed to broiler chicks at varying times during development.

Procedure: Ascusbbr_105932, Ascusbbr_10593, and Ascusbbr_2676 were administered to chicks. A total of 60 chicks were evenly divided into 3 groups of 20 birds. Each group of 20 birds were housed in an independent battery cage with at least one empty cage in between the groups to avoid cross contamination. The three groups were: experimental group 1, experimental group 2, and the control group.

Experimental group 1 received 0.5 mL of a microbe composition containing Ascusbbr_10593, Asucsbbr_2676, and Ascusbbr_105932 suspend in 1×RAMM saline solution via gavage on day 0 of age. Experimental group 2 received 0.5 mL of a microbe composition containing Ascusbbr_10593, Asucsbbr_2676, and Ascusbbr_105932 suspended in 1×RAMM saline solution on day 5 of age via gavage. The control group received 0.5 mL of sterile 1×RAMM saline solution via gavage. Experimental group 1 and experimental group 2 received approximately 1×10⁶ cells of each strain. On day 7, day 11, day 14, and day 18 of age, 4 birds from each group were randomly selected and removed from the cages to be sampled. Each bird had the following organs sampled: cecum, small intestine content, and small intestine scraping via swab. For cecum and small intestine content the samples were collected in a 2 mL tube containing 200 μL of stop solution (95% ethanol and 5% phenol). For the swabs, the 2 mL collection tubes were prefilled with 600 μL of a stop solution-PBS mixture (25% of stop solution (95% ethanol and 5% phenol) and 75% 1× sterile PBS). Swabs were dipped into the stop solution-PBS mixture and then placed into a new, empty 2 mL collection tube for storage. The samples were then stored at −20° C. until shipment and processing.

Nucleic acids were extracted from each sample. Both DNA and RNA were amplified using PCR, and the libraries were prepped for Illumina MiSeq sequencing. After sequencing, the 16S data was analyzed using USEARCH software, and the administered strains were identified in both the experimental groups and the control group. Table 12, Table 13, and Table 14 show the increases and decreases in the abundance of each strain compared to the control group.

Results:

TABLE 12 Changes in abundance of the administered strains in the cecum content of the broilers Day 11 Day 14 Group Ascusbbr_105932 Ascusbbr_1053 Ascusbbr_2676 Ascusbbr_105932 Ascusbbr_10593 Experimental Group 1: − − − − + Day 0 admin Experimental Group 2: − + − − + Day 5 admin Day 14 Day 18 Group Ascusbbr_2676 Ascusbbr_105932 Ascusbbr_10593 Ascusbbr_2676 Experimental Group 1: − − − − Day 0 admin Experimental Group 2: − − − − Day 5 admin

* Day 7 data was omitted because samples had <100 total reads. ‘−’ represents the relative abundance for that sample being lower than or equal to the relative abundance of the control. ‘+’ represents the relative abundance being greater than the relative abundance of the control sample.

TABLE 13 Changes in abundance of the administered strains in the small intestinal content of the broilers Day 7 Day 11 Group Ascusbbr_105932 Ascusbbr_10593 Ascusbbr_2676 Ascusbbr_105932 Ascusbbr_10593 Ascusbbr_2676 Experimental Group 1: − − − − + − Day 0 admin Experimental Group 2: − + − − − − Day 5 admin Day 14 Day 18 Group Ascusbbr_105932 Ascusbbr_10593 Ascusbbr_2676 Ascusbbr_105932 Ascusbbr_10593 Ascusbbr_2676 Experimental Group 1: − − − − − + Day 0 admin Experimental Group 2: − − − − − + Day 5 admin

* ‘−’ represents the relative abundance for that sample being lower than or equal to the relative abundance of the control. ‘+’ represents the relative abundance being greater than the relative abundance of the control sample.

TABLE 14 Changes in abundance of the administered strains in the small intestinal wall scraping of the broilers Day 7 Day 11 Group Ascusbbr_105932 Ascusbbr_10593 Ascusbbr_2676 Ascusbbr_105932 Ascusbbr_10593 Ascusbbr_2676 Experimental Group 1: − − − − − − Day 0 admin Experimental Group 2: − + + − − + Day 5 admin Day 14 Day 18 Group Ascusbbr_105932 Ascusbbr_10593 Ascusbbr_2676 Ascusbbr_105932 Ascusbbr_10593 Ascusbbr_2676 Experimental Group 1: − − − − − − Day 0 admin Experimental Group 2: − − + − − − Day 5 admin

* ‘−’ represents the relative abundance for that sample being lower than or equal to the relative abundance of the control. ‘+’ represents the relative abundance being greater the relative abundance of the control sample.

Discussion:

Ascusbbr_105932 failed to colonize in any of the organs that were tested across all time points. Ascusbbr_10593 seems to establish at a higher abundance than the control in the cecum of experimental group 2. In the cecum of group 2, there was establishment on day 11 and day 14 of age, while on day 18 of age the relative abundance was equal to or less than the relative abundance of the control group. The increase in abundance of Ascusbbr_10593 showed that there was increased colonization of Ascusbbr_10593 as compared to the control. Without continuous administration of Ascusbbr_10593, the microbiota of the cecum returned to a more natural state by day 18 of age. This trend has been shown in multiple animals and studies where there was an attempt to change the natural microbiota. See Preidis et al. (2012. FASEB J. 26:1960-1969), Weimer et al. (2010. J. Dairy Sci. 93:5902-5912), Weimer (2015. Front. Microbiol. 6:1-16), and Weimer et al. (2017. J. Dairy Sci. 100:7165-7182). Ascusbbr_10593 also showed colonization on day 7 of age of the small intestine scrapings in group 2 before the microbiota return to its natural state on day 11 of age. The results of the small intestine scrapings are also mirrored in the small intestine content, showing that there is greater colonization of Ascusbbr_10593 when the chicks were gavaged with at day 5 of age.

Ascusbbr_2676 in experimental group 2 colonized in the small intestine scrapings on day 7 and day 11 of age before it returned to a similar microbiota of the control on day 18 of age. The lack of Ascusbbr_2676 colonization in the small intestine content suggests that Ascusbbr_2676 binding to the mucosal layer through collagen (types-III, IV, and V), gelatin, fibrinogen, lectin, laminin, or vitronectin.

For experimental group 1, where microbes were administered on day 0 of age, there seems to be inconsistent results and lack of evidence of Ascusbbr_10593, Ascusbbr_2676, and Ascusbbr_105932 colonization. This could be due to the anti-microbial properties that a young chick possesses early in its life span within the GI tract. Administration of microbes on day 5 of age compared to day 0 of age seems to benefit the establishment and colonization of Ascus microbes.

REFERENCES

-   Preidis, G. A. et al. Probiotics stimulate enterocyte migration and     microbial diversity in the neonatal mouse intestine. FASEB J. 26,     1960-1969 (2012). -   Weimer, P. J., Stevenson, D. M., Mantovani, H. C. & Man, S. L. C.     Host specificity of the ruminal bacterial community in the dairy cow     following near-total exchange of ruminal contents. J. Dairy Sci. 93,     5902-5912 (2010). -   Weimer, P. J. Redundancy, resilience, and host specificity of the     ruminal microbiota: Implications for engineering improved ruminal     fermentations. Front. Microbiol. 6, 1-16 (2015). -   Weimer, P. J. et al. Transient changes in milk production efficiency     and bacterial community composition resulting from near-total     exchange of ruminal contents between high- and low-efficiency     Holstein cows. J. Dairy Sci. 100, 7165-7182 (2017).

Example II. Lectin-Binding Testing of Broiler Isolates

Immediately after hatching, broiler chicks are protected from pathogens by the antimicrobial properties of egg whites. See Hager et al. (1983. Poultry Science. 62:247-254). After this protection disappears, chicks are constantly challenged with pathogens and never converge on a core microbiome. This leads to high death rates due to necrotic enteritis and chronically inflamed intestinal epithelial. Through competitive exclusion via the founder effect, broiler strains that display collagen and mucin binding have the ability to exclude pathogens. This has been shown in many cases to increase overall immune health and decrease the chronically inflamed intestinal epithelial. See Yadav et al. (2013. Microbiol. Res. 168:639-645). Here, we test 4 strains (strain 1, strain 2, positive control, and negative control) for the ability to bind particular lectins using ELISAs.

The lectin binding assays are designed to identify phenotypic mannose, fucose and N-acetylglucosamine lectin binding via a Sandwich ELISA. Each strain is tested in triplicate and compared to positive and negative controls. The binding is a calcium-dependent lectin binding protein involved in immune defense. The ELISA sandwich assay utilizes the antibody specific for chicken mannose-binding lectin. There are many synonyms to this type of binding including but not limited to Collectin-1, Mannan-binding protein, Mannose-binding lectin, Mannose-binding protein C, MBL2, MBL2_CHICKEN, MBP-C, MBP1. Furthermore, this assay tests for both bacteria that contain both 1 C-type lectin domain and 1 collagen-like domain.

Standard Preparation

Serially diluted standards are prepared fresh prior to use. Broiler MBL standard is used as a positive control in combination with broiler chicken serum/plasma samples. Tubes are mixed gently. 25 ng/mL standards are serially diluted at 200 ul mixing gently at each dilution. Blank controls contain no protein.

Sample and Plate Preparation

All isolated are grown to sufficient turbidity and pelleted through spinning. All samples are split to create technical triplicates for testing, with the suggested dilution for normal serum/plasma: 800 fold.

Assay Protocol

All materials are equilibrated to room temperature all samples and standards are performed in triplicates. 100 uL of each sample and standard are pipetted into the appropriate wells. The plate is covered and incubated at room temperature overnight at 4 degrees C. After incubation samples are washed 4 times with PBS wash buffer and removed through aspiration. 100 ul of prepared biotinylated Human MBL Detection Antibody and then incubated for one hour at room temperature with gentle shaking. 100 ul of 1×HRP-Streptavidin solution is added to each well and for 45 minuets at room temperature with gentle shaking. 100 ul of TMB is added to each well and for 30 minuets at room temperature with gentle shaking. Finally, 50 μL of Stop Solution is added to each well. Optical density at 450 nm is read immediately following.

Anti-Inflammatory to In Vivo Test

Organisms that test positive for binding domains are grown and tested in vivo in broiler chickens through an oral gavage. Broilers are tested for Serum α-1-AGP, CD4+ lymphocytes, CD8+ lymphocytes, cytokines IL8 and TNFSF15, IL17F, iNOS expression, and Gene Expression of tight junction proteins JAM2, occludin, ZO1, and MUC2. See Gadde et al. (2017. Res. Vet Sci. 114:236-243).

Results

Testing of binding assay on strain isolates one and two will likely reveal clear binding in only isolate two (FIG. 6 ). Isolate two is then used to orally gavage broiler chickens. Serum from gavaged chickens are confirmed to be immunologically improved through Serum α-1-AGP, CD4+ lymphocytes, CD8+ lymphocytes, cytokines IL8 and TNFSF15, IL17F, iNOS expression, and Gene Expression of tight junction proteins JAM2, occludin, ZO1, and MUC2 will be compared to control serum with a p-value of 1e-16.

REFERENCES

-   Hager J E, Beane W L. 1983. Posthatch incubation time and early     growth of broiler chickens. Poult Sci 62:247-254. -   Yadav A K, Tyagi A, Kaushik J K, Saklani A C, Grover S, Batish     V K. 2013. Role of surface layer collagen binding protein from     indigenous Lactobacillus plantarum 91 in adhesion and its     anti-adhesion potential against gut pathogen. Microbiol Res     168:639-645. -   Gadde U D, Oh S, Lee Y, Davis E, Zimmerman N, Rehberger T, Lillehoj     H S. 2017. Dietary Bacillus subtilis-based direct-fed microbials     alleviate LPS-induced intestinal immunological stress and improve     intestinal barrier gene expression in commercial broiler chickens.     Res Vet Sci 114:236-243.

Example III. Collagen-Binding Testing of Broiler Isolates

It has long been estabilished that Clostridium perfringens is a major causative agent of necrotic enteritis, a common poultry disease estimated to cost the world $6 billion a year. See Immerseel et al. (2009. Trends Microbiol. 17:32-36) and Wade and Keyburn (2015. World Poultry. 31(7):16-17). “The ability to adhere to the host's intestinal epithelium and to extracellular matrix molecules in the gut are well known strategies used by bacterial enteropathogens,” and it is postulated that C. perfringens uses a similar strategy to colonize poultry intestinal cells through the binding of extracellular matrix molecules including collagen. See Martin and Smyth (2010. Anaerobe. 16(5):533-539). Various studies have illustrated a strong correlation between C. perfringens' ability to adhere to various collagen types and the strain's virulence. See Wade et al. (2016. Vet. Microbiol. 197:53-61). Therefore, a collagen binding assay is designed with the purpose of discovering microorganisms that could competitively inhibit C. perfringens colonization by preferentially binding select collagen motifs that are also adhered to by C. perfringens. Our results will show that our avirulent strain is able to bind collagen types III through V and gelatin with similar or greater affinity than virulent C. perfringens.

This assay based upon a protocol designed by Wade et al., investigating the binding of various bacteria to gelatin and collagen types II, III, IV, V. See Wade et al. (2015. Vet. Microbiol. 180(3-4):299-303).

Solubilizing Collagen and Gelatin

The following stocks are created: 1 mg of collagen type II and IV is added to 50 ml PBS and 0.13 ml acetic acid and shaken overnight at 4° C. 1 mg of collagen type III is added to 48.5 ml PBS and 1.5 ml acetic acid and shaken overnight at 4° C. 1 mg of collagen type V is added to 48.8 ml PBS and 1.2 ml of acetic acid and shaken at room temp for 3 hours. Gelatin is added to 49.7 ml PBS and 0.3 ml acetic acid and shaken at room temp for 3 hours.

Collagen and Gelatin Adherence

50 ul of the 1 mg/50 ml solutions of either: collagen type II, III, IV, V, gelatin, or PBS is added to each well of a 96 well NUNCLON Delta surface treated plate. The plates are then incubated overnight in the dark at 4° C.

Blocking the Wells

A blocking solution is made of Ig of BSA and 20 ul of Tween 20 in 40 ml of PBS. 200 ul of this blocking solution is added to each well of the plate. The plate is incubated for 2 hours in the dark at 4° C. After this each well is rinsed three times with 200 ul of PBS.

Cellular Adhesion

A virulent C. perfringens positive for the cnaA gene, an avirulent gram-positive strain positive for the cnaA gene, and a gram-positive strain negative for the cnaA gene is grown up to late exponential phase in anaerobic TSB+5% defibrinated sheep's blood. 40 ml from these cultures are then centrifuged at 4,300 RCF for 30 minutes at 4° C. Pellets are then washed three times with fresh PBS and cell suspensions are adjusted to an optical density of 0.8 at 600 nm. 50 ul of cell suspension is added to each well and the plate is incubated at room temperature for 2 hours in the dark with agitation. After this, each well is washed three times with 100 ul of fresh PBS.

Crystal Violet Stain

A solution of 0.5% (w/v) of crystal violet in PBS is made. 100 ul of this is added to each well and incubated at room temp in the dark for 5 minutes. Then each well is washed three times with 100 ul of fresh PBS. Cells are then destained with 50 ul of 1:1 ethanol:acetone (v/v) and absorbance of each well is read at 562 nm.

Results

All reported results are corrected by their respective controls. From our results, we expect to see that both cnaA positive strains C. perfringens and Strain 1 have a higher binding affinity for all of the tested proteins than the cnaA negative Strain 2. (FIG. 7 ) This is in agreement with previous data3-5 which shows a correlation between the presence of the cnaA gene and a strain's ability to bind collagen. Furthermore, these results will indicate that Strain 1 has a greater adherence to gelatin and collagen III, IV and V than C. perfringens. Because of this it is possible that Strain 1 could be used as a competitive inhibitor to C. perfringens binding of extracellular matrix molecules in broiler. By inhibiting the colonization of C. perfringens, Strain 1 could reduce the incidence of necrotic enteritis and improve the health of broiler chickens.

REFERENCES

-   Van Immerseel, F., Rood, J. I., Moore, R. J., Titball, R. W., 2009.     Rethinking our understanding of the pathogenesis of necrotic     enteritis in chickens. Trends Microbiol. 17, 32-36. -   Wade, B., Keyburn, A. L., 2015. The true cost of necrotic enteritis.     World Poultry 31 (7), 16-17. -   Thomas G. Martin, Joan A. Smyth, The ability of disease and     non-disease producing strains of Clostridium perfringens from     chickens to adhere to extracellular matrix molecules and Caco-2     cells, In Anaerobe, Volume 16, Issue 5, 2010, Pages 533-539, ISSN     1075-9964, https://doi.org/10.1016/j.anaerobe.2010.07.003. -   Ben Wade, Anthony L. Keyburn, Volker Haring, Mark Ford, Julian I.     Rood, Robert J. Moore, The adherent abilities of Clostridium     perfringens strains are critical for the pathogenesis of avian     necrotic enteritis, In Veterinary Microbiology, Volume 197, 2016,     Pages 53-61 -   B. Wade, A. L. Keyburn, T. Seemann, J. I. Rood, R. J. Moore, Binding     of Clostridium perfringens to collagen correlates with the ability     to cause necrotic enteritis in chickens, In Veterinary Microbiology,     Volume 180, Issues 3-4, 2015, Pages 299-303.

Example III. Collagen-Binding Testing of Broiler Isolates

Purpose:

The objective of this study is to test the ability of formulated microbes to colonize young chicks when mixed into mash feed for 35 days.

Procedure:

Ascusbbr_105932, Ascusbbr_5796, and Ascusbbr_2676 were administered to chicks. A total of 192 chicks were evenly divided into 4 treatment groups. Each treatment group consisted of 3 pens, with each pen containing 16 birds The four groups were: unchallenged control, positive control (all 3 microbes administered via gavage), experimental group 1, and experimental group 2.

Experimental group 1 received a microbial composition containing Ascusbbr_105932, Ascusbbr_2676, and a carrier mixed into feed daily. Experimental group 2 received a microbial composition containing Ascusbbr_105932, Ascusbbr_5796, Ascusbbr_2676, and a carrier mixed into feed daily. Experimental group 1 and experimental group 2 received approximately 1×106 cells of each strain. The positive control received Ascusbbr_105932, Ascusbbr_5796, and Ascusbbr_2676 suspended in 1×RAMM saline solution once on day 5 of age via gavage. The control group received the carrier daily via feed. On day 2, day 7, day 14, day 21, day 28, and day 35 of age, 2 birds from each group were randomly selected and removed from the cages to be sampled. Each bird had the following organs sampled: cecum, small intestine content, and small intestine scraping via swab. For cecum and small intestine content the samples were collected in a 2 mL tube containing 200 μL of stop solution (95% ethanol and 5% phenol). For the swabs, the 2 mL collection tubes were prefilled with 600 μL of a stop solution-PBS mixture (25% of stop solution (95% ethanol and 5% phenol) and 75% 1× sterile PBS). Swabs were dipped into the stop solution-PBS mixture and then placed into a new, empty 2 mL collection tube for storage. The samples were then stored at −20° C. until shipment and processing.

Nucleic acids were extracted from each sample. Both DNA and RNA were amplified using PCR, and the libraries were prepped for Illumina MiSeq sequencing. After sequencing, the 16S data was analyzed using USEARCH software, and the administered strains were identified in both the experimental groups and the control group. Table 12, Table 13, and Table 14 show the increases and decreases in the abundance of each strain compared to the control group.

Results:

Ascusbbr_105932 showed colonization on the small intestine lining by day 7 in experimental group 1, experimental group 2, and the positive control. It was not detected in the unchallenged control.

Ascusbbr_2676 showed colonization in experimental group 1, experimental group 2, and the positive control in the small intestine content and on the small intestine lining. It was not detected in the unchallenged control.

Ascusbbr_5796 showed colonization in experimental group 1, experimental group 2, and the positive control by day 7 in the small intestine content and lining. Its abundance was only detected in the unchallenged control group in the small intestine lining samples.

See FIG. 8 for the depiction of the rate of microbial convergence across the experimental groups. Here, day 35 is assumed to represent the final microbiome of the flock. The distance between the microbiome throughout the experiment was compared to the average, final, day 35 microbiome of the birds. Birds receiving microbes, notably experimental group 2 (3 microbes in feed) and the positive control (oral gavage, 3 microbes) displayed a faster convergence to the final microbiome than experimental group 1 and the unchallenged control.

See FIG. 9 for the final percentage mortality of the experiment. All groups that received microorganisms (positive control, experimental group 1, and experimental group 2) exhibited lower percentage mortality than the control.

Discussion:

Here, native microbes were successfully delivered to the gastrointestinal tract of broiler chickens in a stabilized form via feed. Colonization patterns of the primary target microorganisms were similar to the unstabilized microorganisms utilized in the positive control. Ascusbbr_105932 and Ascusbbr_2676 were only detected in the three groups that received microbes. They were not detected in the unchallenged control. Ascusbbr_5796, however, did appear in all 4 experimental groups despite only being administered to experimental group 2 and the positive control. In the 3 groups that received microbes, Ascusbbr_5796 was detected in the small intestine content and lining. In the unchallenged control, it was only detected in the small intestine lining. The appearance of Ascusbbr_5796 in all 4 treatment groups is unsurprising, as it is a common member of the native broiler chicken microbiome.

Administration of microorganisms was also found to improve the performance of the birds. All three groups that received microorganisms exhibited lower percent mortality than the unchallenged control. Similarly, the two groups that received three microorganisms (experimental group 2 and the positive control), exhibited a faster rate of microbiome maturity than experimental group 1 and the unchallenged control. A more mature microbiome is more resilient to pathogens and infection, so these birds would be more likely to survive an outbreak of a bacterial infection.

TABLE 15 Budapest Treaty Deposits of the Disclosure Depository Accession Number Date of Deposit ATCC PTA-124016 Mar. 2, 2017 ATCC PTA-124039 Mar. 10, 2017 Bigelow PATENT201703001 Mar. 17, 2017 Bigelow PATENT201703002 Mar. 24, 2017 Bigelow PATENT201703003 Mar. 24, 2017 Bigelow PATENT201703004 Mar. 24, 2017 NRRL B-67264 May 16, 2016 NRRL B-67265 May 16, 2016 NRRL B-67266 May 16, 2016 NRRL B-67267 May 16, 2016 NRRL B-67268 May 16, 2016 NRRL B-67269 May 16, 2016 NRRL B-67270 May 16, 2016 NRRL B-67689 Sep. 26, 2018 NRRL B-67690 Sep. 26, 2018 NRRL B-67691 Sep. 26, 2018 NRRL B-67692 Sep. 26, 2018

NUMBERED EMBODIMENTS OF THE DISCLOSURE

Notwithstanding the appended claims, the disclosure sets forth the following numbered embodiments:

-   -   1. A method for stimulating the production of B cells,         stimulating the production of T cells, increasing the length of         villi, reducing the expression of inflammatory cytokines of         poultry, the method comprising:     -   a) administering to a poultry an effective amount of a poultry         supplement comprising:     -   i) a purified microbial population that comprises a bacterium         with a 16S nucleic acid sequence, and/or a fungus with an ITS         nucleic acid sequence, which is at least about 97% identical to         a nucleic acid sequence selected from the group consisting of         SEQ ID NOs:1-387, and said bacterium and/or fungus have a MIC         score of at least about 0.2; and     -   ii) a carrier suitable for poultry administration,     -   wherein the poultry administered the effective amount of the         poultry supplement exhibits an increase in production of B         cells, an increase in production of T cells, an increase in         length of villi, or a decrease in the expression of inflammatory         cytokines, as compared to poultry not having been administered         the supplement.     -   2. The method of embodiment 1, wherein the poultry is a broiler.     -   3. The method according to embodiment 1, wherein the poultry         supplement is stable under ambient conditions for at least one         week.     -   4 The method according to embodiment 1, wherein the poultry         supplement is formulated as an: encapsulation, tablet, capsule,         pill, feed additive, food ingredient, food additive, food         preparation, food supplement, water additive, water-mixed         additive, heat-stabilized additive, moisture-stabilized         additive, consumable solution, consumable spray additive,         consumable solid, consumable gel, injection, suppository,         drench, or combinations thereof.     -   5. The method according to embodiment 1, wherein the poultry         supplement is encapsulated in a polymer or carbohydrate.     -   6, The method according to embodiment 1, wherein the poultry         supplement comprises a glassy matrix comprising the bacterium         and/or the fungus.     -   7. The method according to embodiment 1, wherein the poultry         supplement exhibits a water activity of less than 0.25.     -   8. The method according to embodiment 1, wherein the poultry         supplement is administered one or more times at least one day         post-hatching.     -   9. The method according to embodiment 1, wherein the poultry         supplement is administered one or more times between the day of         hatching and 14 days post-hatching.     -   10. The method according to embodiment 1, wherein the poultry         supplement comprises a first microbial composition and a second         microbial composition.     -   11. The method according to embodiment 10, wherein the first         microbial composition is administered daily beginning at day 4         or 5 post-hatching, and the second microbial composition is         administered daily beginning with the first feed change.     -   12. The method of embodiment 11, wherein the first microbial         composition is no longer administered once the administration of         the second microbial composition begins.     -   13. The method according to embodiment 1, wherein the poultry         supplement comprises:     -   a) a first microbial composition administered one or more times         between the day of hatching, and     -   b) a second microbial composition administered one or more times         between 15 days post-hatching and harvest of the poultry.     -   14. The method according to embodiment 1, wherein administering         comprises: feeding the poultry supplement to the poultry.     -   15. The method according to embodiment 1, wherein administering         comprises: spraying the poultry supplement onto a poultry.     -   16. The method according to embodiment 1, wherein the purified         microbial population is present in the poultry supplement at a         concentration of at least 102 cells.     -   17. The method of embodiment 1, wherein the poultry exhibit an         increase in production of B cells.     -   18. The method of embodiment 17, wherein the B cells are         selected from the group consisting of B-1 cells, B-2 cells,         marginal zone B cells, follicular B cells, memory B cells,         plasma cells, and plasmablasts; or combinations thereof.     -   19. The method of embodiment 1, wherein the poultry exhibit an         increase in production of T cells.     -   20. The method of embodiment 19, wherein the T cells are         selected from the group consisting of gamma delta T cells, alpha         beta T cells, natural killer T cells, regulatory T cells, memory         T cells, cytotoxic T cells helper T cells, and effector T cells;         or combinations thereof.     -   21. The method of embodiment 1, wherein the poultry exhibit an         increase in length of villi.     -   22. The method of embodiment 21, wherein the villi length         increase by at least 1 μM.     -   23. The method of embodiment 22, wherein the villi length         increase by less than 10 μM.     -   24. The method of embodiment 13, wherein the second microbial         composition elicits a thinning of the ileal tissue, a reduction         in pH in the ileum, and/or a reduction in gas production in the         gastrointestinal tract of the poultry.     -   25. The method of embodiment 11, wherein the second microbial         composition elicits a decrease in the variability of the number         of unique species in the gastrointestinal tract of the poultry.     -   26. The method of embodiment 24, wherein the poultry exhibit a         thinning of the ileal tissue.     -   27. The method of embodiment 26, wherein the ileal tissue is         thinned by at least 1 μM.     -   28. The method of embodiment 26, wherein the ileal tissue is         thinned by less than 200 μM.     -   29. The method of embodiment 24, wherein the poultry exhibit a         reduction in pH in the ileum by at least 0.6 pH.     -   30. The method of embodiment 24, wherein the production of gas         in the gastrointestinal tract of the poultry is a reduction of         at least 5%.     -   31. The method of embodiment 25, wherein the decrease in the         variability of the number of unique species is a reduction of         the total number of unique species of microbes in the small         intestine to between about 100 and 400 species.

While preferred embodiments of the present disclosure have been shown and described herein, it will be obvious to those skilled in the art that such embodiments are provided by way of example only. Numerous variations, changes, and substitutions will now occur to those skilled in the art without departing from the disclosure. It should be understood that various alternatives to the embodiments of the disclosure described herein may be employed in practicing the disclosure. It is intended that the following Claims define the scope of the disclosure and that methods and structures within the scope of these claims and their equivalents be covered thereby.

INCORPORATION BY REFERENCE

All references, articles, publications, patents, patent publications, and patent applications cited herein are incorporated by reference in their entireties for all purposes.

However, mention of any reference, article, publication, patent, patent publication, and patent application cited herein is not, and should not be taken as, an acknowledgment or any form of suggestion that they constitute valid prior art or form part of the common general knowledge in any country in the world. 

The invention claimed is:
 1. A method for improving one or more desirable traits in a fowl, the method comprising administering to the fowl an effective amount of a microbial composition comprising: (a) a purified microbial population that comprises: (i) a bacterium with a 16S nucleic acid sequence that shares at least 97% sequence identity with SEQ ID NO: 386, and/or (ii) a bacterium with a 16S nucleic acid sequence that shares at least 97% sequence identity with SEQ ID NO: 387, and (b) a carrier suitable for fowl administration; wherein the purified microbial population is present in the microbial composition in an amount effective to improve the one or more desirable traits as compared to a fowl not having been administered the microbial composition.
 2. The method of claim 1, wherein the fowl is a broiler.
 3. The method of claim 1, wherein the bacterium has a maximal information coefficient (MIC) score of at least about 0.1.
 4. The method of claim 1, wherein the purified microbial population comprises a bacterium with a 16S nucleic acid sequence sharing at least 97% sequence identity with SEQ ID NO:386.
 5. The method of claim 1, wherein the purified microbial population comprises a bacterium with a 16S nucleic acid sequence sharing at least 97% sequence identity with SEQ ID NO:387.
 6. The method of claim 1, wherein the purified microbial population further comprises one or more bacteria with a 16S nucleic acid sequence sharing at least 97% sequence identity with a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 1-50 and 59-385; and/or one or more fungi with an internal transcribed spacer (ITS) nucleic acid sequence that shares at least about 97% sequence identity with a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 51-58.
 7. The method of claim 1, wherein the purified microbial population comprises: a bacterium with a 16S nucleic acid sequence sharing at least 98% sequence identity with SEQ ID NO:386 and/or a bacterium with a 16S nucleic acid sequence sharing at least 98% sequence identity with SEQ ID NO:387.
 8. The method of claim 1, wherein the purified microbial population comprises: a bacterium with a 16S nucleic acid sequence sharing at least 99% sequence identity with SEQ ID NO:386 and/or a bacterium with a 16S nucleic acid sequence sharing at least 99% sequence identity with SEQ ID NO:387.
 9. The method of claim 1, wherein the purified microbial population further comprises one or more bacteria with a 16S nucleic acid sequence sharing at least 98% sequence identity with a nucleic acid sequence selected from the group consisting of: SEQ ID NOs: 1-50 and 59-385; and/or one or more fungi with an ITS nucleic acid sequence that shares at least 98% sequence identity with a nucleic acid sequence selected from the group consisting of: SEQ ID NOs: 51-58.
 10. The method of claim 1, wherein the purified microbial population further comprises one or more bacteria with a 16S nucleic acid sequence sharing at least 97% sequence identity with a nucleic acid sequence selected from the group consisting of: SEQ ID NO:3, SEQ ID NO: 13, SEQ ID NO: 369, SEQ ID NO: 370, and SEQ ID NO:
 374. 11. The method of claim 1, wherein the purified microbial population comprises: a bacterium with a 16S nucleic acid sequence of SEQ ID NO:386 and/or a bacterium with a 16S nucleic acid sequence of SEQ ID NO:387.
 12. The method of claim 1, wherein the purified microbial population comprises: a bacterium with a 16S nucleic acid sequence comprising SEQ ID NO:386 or a bacterium with a 16S nucleic acid sequence comprising SEQ ID NO:387.
 13. The method of claim 1, wherein the purified microbial population comprises one or more bacteria with a 16S nucleic acid sequence sharing at least 98% sequence identity with a nucleic acid sequence selected from the group consisting of: SEQ ID NO:3, SEQ ID NO: 13, SEQ ID NO: 369, SEQ ID NO: 370, and SEQ ID NO:
 374. 14. The method of claim 1, wherein the microbial composition is formulated as an encapsulation, tablet, capsule, pill, feed additive, food ingredient, food preparation, food supplement, water additive, water-mixed additive, heat-stabilized additive, moisture-stabilized additive, pre-pelleted feed additive, pelleted feed additive, post-pelleting-applied feed additive, consumable solution, consumable spray additive, consumable solid, consumable gel, injection, suppository, drench, bolus, or combination thereof.
 15. The method of claim 1, wherein the improvement of the one or more desirable traits is an improvement in antimicrobial production.
 16. The method of claim 15, wherein the improvement of antimicrobial production is an improvement of antimicrobial production in the gastrointestinal tract.
 17. The method of claim 1, wherein the administering a purified microbial population comprises administering a first microbial composition and a second microbial composition.
 18. The method of claim 1, wherein the microbial composition elicits a decrease in the variability of the number of unique species in the gastrointestinal tract.
 19. The method of claim 18, wherein the decrease in the variability of the number of unique species is a reduction of the total number of unique species of microbes to between about 50 and 400 species.
 20. The method of claim 1, wherein the purified microbial population further comprises one or more bacteria with a 16S nucleic acid sequence sharing at least 99% sequence identity with a nucleic acid sequence selected from the group consisting of: SEQ ID NOs: 1-50 and 59-385; and/or one or more fungi with an ITS nucleic acid sequence that shares at least 99% sequence identity with a nucleic acid sequence selected from the group consisting of: SEQ ID NOs: 51-58.
 21. The method of claim 1, wherein the purified microbial population further comprises one or more bacteria with a 16S nucleic acid sequence sharing at least 99% sequence identity with a nucleic acid sequence selected from the group consisting of: SEQ ID NO:3, SEQ ID NO: 13, SEQ ID NO: 369, SEQ ID NO: 370, and SEQ ID NO:
 374. 22. The method of claim 1, wherein the improvement of the one or more desirable traits is an improvement in the innate immune response, an improvement in incidence of normal gastrointestinal morphology, an improvement in growth rate, an improvement in total body mass, an improvement in feed conversion ratio, an improvement in pathogen exclusion, an improvement in competitive exclusion against pathogens, a reduction in mortality, a reduction in flock variability, an improvement in antimicrobial production, an improvement in stimulating the production of B cells, an improvement in stimulating the production of lymphocytes, an improvement in length of villi, and/or an improvement in expression of inflammatory cytokines.
 23. The method of claim 1, wherein the purified microbial population further comprises one or more bacteria with a 16S nucleic acid sequence selected from the group consisting of: SEQ ID NOs: 1-50 and 59-385; and/or one or more fungi with an ITS nucleic acid sequence selected from the group consisting of: SEQ ID NOs: 51-58.
 24. The method of claim 1, wherein the purified microbial population further comprises one or more bacteria with a 16S nucleic acid sequence selected from the group consisting of: SEQ ID NO:3, SEQ ID NO: 13, SEQ ID NO: 369, SEQ ID NO: 374, and SEQ ID NO:
 370. 25. The method of claim 1, wherein the purified microbial population comprises a bacterium with a 16S nucleic acid sequence sharing at least 98% sequence identity with SEQ ID NO:387.
 26. The method of claim 1, wherein the purified microbial population comprises a bacterium with a 16S nucleic acid sequence sharing at least 99% sequence identity with SEQ ID NO:387.
 27. The method of claim 1, wherein the purified microbial population comprises a bacterium with a 16S nucleic acid sequence of SEQ ID NO:387.
 28. The method of claim 1, wherein the purified microbial population comprises a bacterium as deposited as NRRL B-67691.
 29. The method of claim 1, wherein the carrier is calcium carbonate.
 30. The method of claim 1, wherein the microbial composition is formulated as a pelleted feed additive.
 31. The method of claim 1, wherein the purified microbial population comprises at least 10² cells. 